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<a class="post-title-link" href="/2017/08/12/Python-生物信息学数据管理（十五）/" itemprop="url">Python 生物信息学数据管理（十五）</a></h1>
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<p>这一期，通过几组题目，我们一起对上一期的内容进行回顾，通过定义函数，调用函数的方式解决问题。<br>
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<p>这一期开始，将开始介绍模块化编程的知识，使用函数更好的组织程序</p>
<ul>
<li>编写自己的函数</li>
<li>从蛋白质结构的坐标中提取序列</li>
<li>有选择性地从PDB文件中提取信息</li>
<li>计算蛋白质或DNA三维结构中的原子间距
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<p>该期，我们将通过几组练习题，巩固上一期学习的模式匹配内容<br>
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2017-08-08
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<p>这一期，我们将介绍Python中的<code>模式匹配</code>，并将其应用于文本的挖掘</p>
<ul>
<li>使用正则表达式表达共有序列</li>
<li>使用Python中的正则表达式工具在字符串中搜索子字符串</li>
<li>在蛋白质中搜索功能性模体(motif)</li>
<li>在文本（例如科学摘要）中搜索给定的词或一组词</li>
<li>在核苷酸序列（例如，转录因子或miRNA的结合位点）中识别模体</li>
</ul>
<p>按照惯例，我们将先介绍一个案例</p>
<h2 id="案例：在蛋白质序列中搜索磷酸化模体"><a href="#案例：在蛋白质序列中搜索磷酸化模体" class="headerlink" title="案例：在蛋白质序列中搜索磷酸化模体"></a>案例：在蛋白质序列中搜索磷酸化模体</h2><p>序列功能模体(sequence functional motif)：能形式功能的短氨基酸或核苷酸序列，含有一个或多个残基的功能区。磷酸化位点、甘露糖基化位点、识别模体、糖基化位点、转录结合位点等都是功能性模体的典型范例。<br>先看一个正则表达式的小例子<br><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div></pre></td><td class="code"><pre><div class="line">'AFL','GFI','AYI','GWI','GFI','AWI','GWL','GYL'</div><div class="line">#我们可以通过以下单一的方式，表示上述字符</div><div class="line">[AG][FYW][IL]</div></pre></td></tr></table></figure></p>
<p>开源致力于功能性模体：<br><a href="http://elm.eu.org" target="_blank" rel="external">ELM</a>和<a href="http://prosite.expasy.org" target="_blank" rel="external">PROSITE</a></p>
<p><a href="http://prosite.expasy.org/scanprosite" target="_blank" rel="external">ScanProsite</a><br>搜索一套蛋白质序列或一组序列是否存在功能性模体，可以进而推断蛋白质的功能。<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> re</div><div class="line">seq = <span class="string">'VSVLTMFRYAGLDRLYMLVGTQLAAIIHGVALPLMMLI'</span></div><div class="line"><span class="comment">#re.compile()函数返回正则表达式</span></div><div class="line">pattern = re.compile(<span class="string">'[ST]Q'</span>)</div><div class="line">match = pattern.search(seq)</div><div class="line"><span class="keyword">if</span> match:</div><div class="line"> print(<span class="string">'%10s'</span> % (seq[match.start()<span class="number">-4</span>:match.end()+<span class="number">4</span>]))</div><div class="line"> print(<span class="string">'%6s'</span> % match.group())</div><div class="line"><span class="keyword">else</span>:</div><div class="line"> print(<span class="string">'no match'</span>)</div></pre></td></tr></table></figure></p>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div></pre></td><td class="code"><pre><div class="line">MLVGTQLAAI</div><div class="line"> TQ</div></pre></td></tr></table></figure>
<h2 id="命令的含义"><a href="#命令的含义" class="headerlink" title="命令的含义"></a>命令的含义</h2><h3 id="编译正则表达式"><a href="#编译正则表达式" class="headerlink" title="编译正则表达式"></a>编译正则表达式</h3><p><code>compile()</code>编译字符串并把它转换成<code>正则表达对象(RegexpObject)</code><br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div></pre></td><td class="code"><pre><div class="line"><span class="meta">>>> </span><span class="keyword">import</span> re</div><div class="line"><span class="meta">>>> </span>regexp = re.compile(<span class="string">'[ST]Q'</span>)</div><div class="line"><span class="meta">>>> </span>regexp</div><div class="line">re.compile(<span class="string">'[ST]Q'</span>)</div></pre></td></tr></table></figure></p>
<p>当然，字符串，也可以记录在变量中<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div></pre></td><td class="code"><pre><div class="line"><span class="meta">>>> </span>motif = <span class="string">'[ST]Q'</span></div><div class="line"><span class="meta">>>> </span>regexp = re.compile(motif)</div><div class="line"><span class="meta">>>> </span>regexp</div><div class="line">re.compile(<span class="string">'[ST]Q'</span>)</div></pre></td></tr></table></figure></p>
<p>我们可以传递参数(编译标志)到<code>compile()</code>方法，总而改变正则表达式某些方面的细节<br>例如，可以忽略大小写：<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div></pre></td><td class="code"><pre><div class="line"><span class="meta">>>> </span>regrxp = re.compile(motif,re.IGNORECASE)</div><div class="line"><span class="meta">>>> </span>regrxp</div><div class="line">re.compile(<span class="string">'[ST]Q'</span>, re.IGNORECASE)</div></pre></td></tr></table></figure></p>
<h3 id="模式匹配"><a href="#模式匹配" class="headerlink" title="模式匹配"></a>模式匹配</h3><p>检验正则表达式是否正确的<a href="http://www.regexplanet.com/simple/" target="_blank" rel="external">在线工具</a><br><code>search()</code>函数扫描字符串并寻找正则表达式第一次匹配的位置，其返回的每个序列最多只能有一个单一匹配对象。<code>group()</code>方法打印第一个匹配的对象。<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> re</div><div class="line">seq = <span class="string">'RQSAMGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQRPSKP'</span></div><div class="line">motif = <span class="string">'R.[ST][^P]'</span></div><div class="line">pattern = re.compile(motif)</div><div class="line">print(pattern)</div><div class="line">match = pattern.search(seq)</div><div class="line">print(match)</div><div class="line">print(match.group())</div></pre></td></tr></table></figure></p>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div></pre></td><td class="code"><pre><div class="line">re.compile('R.[ST][^P]')</div><div class="line"><_sre.SRE_Match object; span=(0, 4), match='RQSA'></div><div class="line">RQSA</div></pre></td></tr></table></figure>
<p><code>search()</code>方法返回<code>Match object</code>而并非直接返回匹配的字符串，其中编码了匹配的子字符串，以及开始和结束的位置</p>
<ul>
<li><code>match.group()</code> 返回匹配字符串</li>
<li><code>match.span()</code> 返回匹配结果的包含<code>起点和终点</code>位置的元组</li>
<li><code>match.start()</code> 返回匹配结果的起始位置</li>
<li><code>match.start()</code> 返回匹配结果的终止位置</li>
</ul>
<p>若只从序列的第一位置寻找正则表达式匹配，则使用<code>match()</code>方法<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> re</div><div class="line">seq = <span class="string">'RQSAMGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQRPSKP'</span></div><div class="line">motif = <span class="string">'R.[ST][^P]'</span></div><div class="line">pattern = re.compile(motif)</div><div class="line">print(pattern)</div><div class="line">match = pattern.match(seq)</div><div class="line">print(match)</div><div class="line">print(match.group())</div></pre></td></tr></table></figure></p>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div></pre></td><td class="code"><pre><div class="line">re.compile('R.[ST][^P]')</div><div class="line"><_sre.SRE_Match object; span=(0, 4), match='RQSA'></div><div class="line">RQSA</div></pre></td></tr></table></figure>
<p><code>search()</code>及<code>match()</code>方法返回<code>匹配对象</code>，该对象可以通过<code>匹配对象</code>方法传递给变量<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div></pre></td><td class="code"><pre><div class="line"><span class="meta">>>> </span>match.span()</div><div class="line">(<span class="number">0</span>, <span class="number">4</span>)</div><div class="line"><span class="meta">>>> </span>match.start()</div><div class="line"><span class="number">0</span></div><div class="line"><span class="meta">>>> </span>match.end()</div><div class="line"><span class="number">4</span></div></pre></td></tr></table></figure></p>
<p>我们也可以搜索所有匹配</p>
<ul>
<li><code>findall()</code> 返回包含所有匹配的一个字符串列表</li>
<li><code>finditer()</code> 以<code>迭代器</code>的形式返回，可以通过<code>for</code>遍历</li>
</ul>
<figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> re</div><div class="line">seq = <span class="string">'RQSAMGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQRPSKP'</span></div><div class="line">motif = <span class="string">'R.[ST][^P]'</span></div><div class="line">pattern = re.compile(motif)</div><div class="line">print(pattern)</div><div class="line">all = pattern.findall(seq)</div><div class="line">print(all)</div><div class="line"></div><div class="line">iter = pattern.finditer(seq)</div><div class="line"><span class="keyword">for</span> s <span class="keyword">in</span> iter:</div><div class="line"> print(s.group())</div><div class="line"> print(s.span())</div><div class="line"> print(s.start())</div><div class="line"> print(s.end())</div></pre></td></tr></table></figure>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div></pre></td><td class="code"><pre><div class="line">re.compile('R.[ST][^P]')</div><div class="line">['RQSA', 'RRSL', 'RPSK']</div><div class="line">RQSA</div><div class="line">(0, 4)</div><div class="line">0</div><div class="line">4</div><div class="line">RRSL</div><div class="line">(18, 22)</div><div class="line">18</div><div class="line">22</div><div class="line">RPSK</div><div class="line">(40, 44)</div><div class="line">40</div><div class="line">44</div></pre></td></tr></table></figure>
<h3 id="分组"><a href="#分组" class="headerlink" title="分组"></a>分组</h3><p>将一个正则表达式分解为若干组<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> re</div><div class="line">seq = <span class="string">'QSAMGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQRPSKP'</span></div><div class="line">pattern1 = re.compile(<span class="string">'R(.)[ST][^P]'</span>)</div><div class="line">match1 = pattern1.search(seq)</div><div class="line">print(match1.group())</div><div class="line">print(match1.group(<span class="number">1</span>))</div><div class="line"></div><div class="line">pattern2 = re.compile(<span class="string">'R(.{0,3})[ST][^P]'</span>)</div><div class="line">match2 = pattern2.search(seq)</div><div class="line">print(match2.group())</div><div class="line">print(match2.group(<span class="number">1</span>))</div></pre></td></tr></table></figure></p>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div></pre></td><td class="code"><pre><div class="line">RRSL</div><div class="line">R</div><div class="line">RRRSL</div><div class="line">RR</div></pre></td></tr></table></figure>
<p><code>group()方法</code>不填写参数或参数等于0，返回完全匹配的子字符串；子组以从左到右编号，向右递增编号(从1开始)<br><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div></pre></td><td class="code"><pre><div class="line">**注意** 子组可以嵌套，为了得到对应的号码，要计算从左至右有多少左圆括号。</div><div class="line">```Python</div><div class="line">>>> import re</div><div class="line">>>> p = re.compile('(a(b)c)d')</div><div class="line">>>> m = p.match('abcd')</div><div class="line">>>> m.group(0)</div><div class="line">'abcd'</div><div class="line">>>> m.group(1)</div><div class="line">'abc'</div><div class="line">>>> m.group(2)</div><div class="line">'b'</div></pre></td></tr></table></figure></p>
<p>向<code>group()</code>传递多个参数，将返回包含各组的值对应的元组<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div></pre></td><td class="code"><pre><div class="line"><span class="meta">>>> </span>m.group(<span class="number">1</span>,<span class="number">2</span>,<span class="number">1</span>)</div><div class="line">(<span class="string">'abc'</span>, <span class="string">'b'</span>, <span class="string">'abc'</span>)</div></pre></td></tr></table></figure></p>
<p><code>groups()</code>返回所有与<code>子组</code>相关的子字符串<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div></pre></td><td class="code"><pre><div class="line"><span class="meta">>>> </span>m.groups()</div><div class="line">(<span class="string">'abc'</span>, <span class="string">'b'</span>)</div></pre></td></tr></table></figure></p>
<p>还可以向每个子组分配名称即<code>?P<名></code>，以便选择性的检索其内容即<code>group(<名>)</code><br>实现代码如下：<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> re</div><div class="line">seq = <span class="string">'QSAMGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQRPSKP'</span></div><div class="line">motif = <span class="string">'R(?P<w1>.{0,3})[ST](?P<w2>[^P])'</span></div><div class="line">pattern = re.compile(motif)</div><div class="line">match = pattern.search(seq)</div><div class="line">print(match.group())</div><div class="line">print(match.group(<span class="string">'w1'</span>))</div><div class="line">print(match.group(<span class="string">'w2'</span>))</div></pre></td></tr></table></figure></p>
<p>输出结果如下：<br><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div></pre></td><td class="code"><pre><div class="line">RRRSL</div><div class="line">RR</div><div class="line">L</div></pre></td></tr></table></figure></p>
<h3 id="修改字符串"><a href="#修改字符串" class="headerlink" title="修改字符串"></a>修改字符串</h3><ul>
<li><code>split(s)</code> 把字符串分割成列表，用RE即<code>s</code>匹配进行分割</li>
<li><code>sub(r,s)</code> 找到所有RE匹配的子串，替换成不同的子串</li>
<li><code>subn(r,s)</code> 与sub()一样，但是返回新字符串的替换的数目</li>
</ul>
<h4 id="split-s"><a href="#split-s" class="headerlink" title="split(s)"></a><code>split(s)</code></h4><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> re</div><div class="line"></div><div class="line">separator = re.compile(<span class="string">'\|'</span>)</div><div class="line"></div><div class="line"><span class="comment"># split</span></div><div class="line">annotation = <span class="string">'ATOM:CA|RES:ALA|CHAIN:B|NUMRES:166'</span></div><div class="line">columns = separator.split(annotation)</div><div class="line">print(columns)</div></pre></td></tr></table></figure>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div></pre></td><td class="code"><pre><div class="line">['ATOM:CA', 'RES:ALA', 'CHAIN:B', 'NUMRES:166']</div></pre></td></tr></table></figure>
<h4 id="sub-r-s-c"><a href="#sub-r-s-c" class="headerlink" title="sub(r,s,[c])"></a><code>sub(r,s,[c])</code></h4><p><code>s</code>字符串中没有重叠出现的给定模式，将被<code>r</code>替换(若可选参数<code>c</code>未被指定)<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> re</div><div class="line"></div><div class="line">separator = re.compile(<span class="string">'\|'</span>)</div><div class="line"></div><div class="line">annotation = <span class="string">'ATOM:CA|RES:ALA|CHAIN:B|NUMRES:166'</span></div><div class="line">columns = separator.split(annotation)</div><div class="line"><span class="comment"># replace</span></div><div class="line">new_annotation = separator.sub(<span class="string">'@'</span>, annotation)</div><div class="line">print(new_annotation)</div><div class="line"></div><div class="line">new_annotation2 = separator.sub(<span class="string">'@'</span>, annotation, <span class="number">2</span>)</div><div class="line">print(new_annotation2)</div></pre></td></tr></table></figure></p>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div></pre></td><td class="code"><pre><div class="line">ATOM:CA@RES:ALA@CHAIN:B@NUMRES:166</div><div class="line">ATOM:CA@RES:ALA@CHAIN:B|NUMRES:166</div></pre></td></tr></table></figure>
<h4 id="subn-r-s-c"><a href="#subn-r-s-c" class="headerlink" title="subn(r,s,[c])"></a><code>subn(r,s,[c])</code></h4><p>返回含有两个元件的元组：<code>新的字符串</code>和<code>发生替代的数量</code><br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div></pre></td><td class="code"><pre><div class="line"><span class="meta">>>> </span>new_annotion = separator.subn(<span class="string">'@'</span>,annotation)</div><div class="line"><span class="meta">>>> </span>print(new_annotion)</div><div class="line">(<span class="string">'ATOM:CA@RES:ALA@CHAIN:B@NUMRES:166'</span>, <span class="number">3</span>)</div></pre></td></tr></table></figure></p>
<h2 id="字符和元字符"><a href="#字符和元字符" class="headerlink" title="字符和元字符"></a>字符和元字符</h2><ul>
<li><code>[^a]</code> 除了a以外的字符</li>
<li><code>^[a]</code> a只匹配s的首位</li>
<li><code>()</code> 在正则表达式中创建子组</li>
<li><code>*</code> 匹配零次或多次</li>
<li><code>+</code> 匹配一次或者多次</li>
<li><code>?</code> 前面的字符可以匹配零次或一次</li>
<li><code>{m,n}</code> 该限定符表示至少m个，至多n个重复可以被匹配</li>
<li><code>$</code> 匹配末位为s的情况</li>
<li><code>\d</code> [0~9]</li>
<li><code>\D</code> [^0~9]</li>
<li><code>\s</code> [\t\n\r\f\v]</li>
<li><code>\w</code> [a~zA~Z0~9]</li>
</ul>
<h2 id="grep：在文件中搜索词的UNIX-Linux命令"><a href="#grep：在文件中搜索词的UNIX-Linux命令" class="headerlink" title="grep：在文件中搜索词的UNIX/Linux命令"></a>grep：在文件中搜索词的UNIX/Linux命令</h2><figure class="highlight bash"><table><tr><td class="gutter"><pre><div class="line">1</div></pre></td><td class="code"><pre><div class="line">$ grep ArticleTile PMID.html</div></pre></td></tr></table></figure>
<p>使用<code>*</code>表示任何字符<br><figure class="highlight bash"><table><tr><td class="gutter"><pre><div class="line">1</div></pre></td><td class="code"><pre><div class="line">$ grep Ar*le mytext.txt</div></pre></td></tr></table></figure></p>
<p>所有以<code>></code>开头的行<br><figure class="highlight bash"><table><tr><td class="gutter"><pre><div class="line">1</div></pre></td><td class="code"><pre><div class="line">$ grep ^<span class="string">'>'</span> 3G5U.fasta</div></pre></td></tr></table></figure></p>
<h2 id="示例"><a href="#示例" class="headerlink" title="示例"></a>示例</h2><p>接下来，我们结合一些示例来体会正则表达式的应用场景</p>
<h3 id="将PROSITE正则表达式转换为Python正则表达式"><a href="#将PROSITE正则表达式转换为Python正则表达式" class="headerlink" title="将PROSITE正则表达式转换为Python正则表达式"></a>将<code>PROSITE</code>正则表达式转换为Python正则表达式</h3><p><a href="http://prosite.expasy.org" target="_blank" rel="external">PROSITE</a>是蛋白质域、蛋白质家族和蛋白质功能位点的资源库。<br>两种表示方法：</p>
<ul>
<li>签名模式(即正则表达式)</li>
<li>配置文件(即位置特异性氨基酸的权重和间隙罚分组成的表)</li>
</ul>
<p>实现代码如下：<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div></pre></td><td class="code"><pre><div class="line">pattern = <span class="string">'[DEQN]-x-[DEQN](2)-C-x(3,14)-C-x(3,7)-C-x-[DN]-x(4)-[FY]-x-C'</span></div><div class="line">pattern = pattern.replace(<span class="string">'{'</span>, <span class="string">'[^'</span>)</div><div class="line">pattern = pattern.replace(<span class="string">'}'</span>, <span class="string">']'</span>)</div><div class="line">pattern = pattern.replace(<span class="string">'('</span>, <span class="string">'{'</span>)</div><div class="line">pattern = pattern.replace(<span class="string">')'</span>, <span class="string">'}'</span>)</div><div class="line">pattern = pattern.replace(<span class="string">'-'</span>, <span class="string">''</span>)</div><div class="line">pattern = pattern.replace(<span class="string">'x'</span>, <span class="string">'.'</span>)</div><div class="line">pattern = pattern.replace(<span class="string">'>'</span>, <span class="string">'$'</span>)</div><div class="line">pattern = pattern.replace(<span class="string">'<'</span>, <span class="string">'^'</span>)</div><div class="line">print(pattern)</div></pre></td></tr></table></figure></p>
<p>输出结果如下：<br><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div></pre></td><td class="code"><pre><div class="line">[DEQN].[DEQN]{2}C.{3,14}C.{3,7}C.[DN].{4}[FY].C</div></pre></td></tr></table></figure></p>
<h3 id="在基因组序列中找到转录因子结合位点"><a href="#在基因组序列中找到转录因子结合位点" class="headerlink" title="在基因组序列中找到转录因子结合位点"></a>在基因组序列中找到转录因子结合位点</h3><ul>
<li>基因组的核苷酸序列文本文件</li>
<li>其格式可以通过计算机程序读取的<code>TFBS</code>列表</li>
</ul>
<p><code>TFBS</code>列表<br><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div></pre></td><td class="code"><pre><div class="line">UAS(G)-pMH100 CGGAGTACTGTCCTCCG ! J Mol Biol 209: 423-32 (1989)</div><div class="line">TFIIIC-Xls-50 TGGATGGGAG ! EMBO J 6: 3057-63 (1987)</div><div class="line">HSE_CS_inver0 CTNGAANNTTCNAG ! Cell 30: 517-28 (1982)</div><div class="line">ZDNA_CS 0 GCGTGTGCA ! Nature 303: 674-9 (1983)</div><div class="line">GCN4-his3-180 ATGACTCAT ! Science 234: 451-7 (1986)</div></pre></td></tr></table></figure></p>
<p><code>genome</code><br><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div></pre></td><td class="code"><pre><div class="line">CGGAGTACTGTCCTCCGTGGATGGGAGCTNGAANNTTCNAGGCGTGTGCAATGACTCAT</div><div class="line">CGGAGTACTGTCCTCCGTGGATGGGAGCTNGAANNTTCNAGGCGTGTGCAATGACTCAT</div><div class="line">CGGAGTACTGTCCTCCGTGGATGGGAGCTNGAANNTTCNAGGCGTGTGCAATGACTCAT</div><div class="line">CGGAGTACTGTCCTCCGTGGATGGGAGCTNGAANNTTCNAGGCGTGTGCAATGACTCAT</div><div class="line">CGGAGTACTGTCCTCCGTGGATGGGAGCTNGAANNTTCNAGGCGTGTGCAATGACTCAT</div><div class="line">CGGAGTACTGTCCTCCGTGGATGGGAGCTNGAANNTTCNAGGCGTGTGCAATGACTCAT</div><div class="line">CGGAGTACTGTCCTCCGTGGATGGGAGCTNGAANNTTCNAGGCGTGTGCAATGACTCAT</div><div class="line">CGGAGTACTGTCCTCCGTGGATGGGAGCTNGAANNTTCNAGGCGTGTGCAATGACTCAT</div></pre></td></tr></table></figure></p>
<p>实现代码如下：<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div><div class="line">17</div><div class="line">18</div><div class="line">19</div><div class="line">20</div><div class="line">21</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> os</div><div class="line"><span class="keyword">import</span> re</div><div class="line">os.chdir(<span class="string">"F:/Python_biologist"</span>)</div><div class="line">genome_seq = open(<span class="string">'genome.txt'</span>).read()</div><div class="line"><span class="comment"># read TFBS patterns</span></div><div class="line">sites = []</div><div class="line"><span class="keyword">for</span> line <span class="keyword">in</span> open(<span class="string">'TFBS.txt'</span>,<span class="string">'r'</span>):</div><div class="line"> fields = line.split( )</div><div class="line"> tf = fields[<span class="number">0</span>]</div><div class="line"> site = fields[<span class="number">1</span>]</div><div class="line"> sites.append((tf,site))</div><div class="line"></div><div class="line"><span class="comment"># match all TF's to the genome and print matches</span></div><div class="line"><span class="keyword">for</span> tf,site <span class="keyword">in</span> sites:</div><div class="line"> tfbs_regexp = re.compile(site)</div><div class="line"> all_matches = tfbs_regexp.findall(genome_seq)</div><div class="line"> matches = tfbs_regexp.finditer(genome_seq)</div><div class="line"> <span class="keyword">if</span> all_matches:</div><div class="line"> print(tf,<span class="string">':'</span>)</div><div class="line"> <span class="keyword">for</span> tfbs <span class="keyword">in</span> matches:</div><div class="line"> print(<span class="string">'\t'</span>,tfbs.group(),tfbs.start(),tfbs.end())</div></pre></td></tr></table></figure></p>
<p>输出结果如下：<br><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div><div class="line">17</div><div class="line">18</div><div class="line">19</div><div class="line">20</div><div class="line">21</div><div class="line">22</div><div class="line">23</div><div class="line">24</div><div class="line">25</div><div class="line">26</div><div class="line">27</div><div class="line">28</div><div class="line">29</div><div class="line">30</div><div class="line">31</div><div class="line">32</div><div class="line">33</div><div class="line">34</div><div class="line">35</div><div class="line">36</div></pre></td><td class="code"><pre><div class="line">UAS(G)-pMH100 :</div><div class="line"> CGGAGTACTGTCCTCCG 0 17</div><div class="line"> CGGAGTACTGTCCTCCG 60 77</div><div class="line"> CGGAGTACTGTCCTCCG 120 137</div><div class="line"> CGGAGTACTGTCCTCCG 180 197</div><div class="line"> CGGAGTACTGTCCTCCG 240 257</div><div class="line"> CGGAGTACTGTCCTCCG 300 317</div><div class="line"> CGGAGTACTGTCCTCCG 360 377</div><div class="line"> CGGAGTACTGTCCTCCG 420 437</div><div class="line">TFIIIC-Xls-50 :</div><div class="line"> TGGATGGGAG 17 27</div><div class="line"> TGGATGGGAG 77 87</div><div class="line"> TGGATGGGAG 137 147</div><div class="line"> TGGATGGGAG 197 207</div><div class="line"> TGGATGGGAG 257 267</div><div class="line"> TGGATGGGAG 317 327</div><div class="line"> TGGATGGGAG 377 387</div><div class="line"> TGGATGGGAG 437 447</div><div class="line">HSE_CS_inver0 :</div><div class="line"> CTNGAANNTTCNAG 27 41</div><div class="line"> CTNGAANNTTCNAG 87 101</div><div class="line"> CTNGAANNTTCNAG 147 161</div><div class="line"> CTNGAANNTTCNAG 207 221</div><div class="line"> CTNGAANNTTCNAG 267 281</div><div class="line"> CTNGAANNTTCNAG 327 341</div><div class="line"> CTNGAANNTTCNAG 387 401</div><div class="line"> CTNGAANNTTCNAG 447 461</div><div class="line">GCN4-his3-180 :</div><div class="line"> ATGACTCAT 50 59</div><div class="line"> ATGACTCAT 110 119</div><div class="line"> ATGACTCAT 170 179</div><div class="line"> ATGACTCAT 230 239</div><div class="line"> ATGACTCAT 290 299</div><div class="line"> ATGACTCAT 350 359</div><div class="line"> ATGACTCAT 410 419</div><div class="line"> ATGACTCAT 470 479</div></pre></td></tr></table></figure></p>
<h3 id="从PubMed的HTML页面提取标题和摘要文本"><a href="#从PubMed的HTML页面提取标题和摘要文本" class="headerlink" title="从PubMed的HTML页面提取标题和摘要文本"></a>从PubMed的HTML页面提取标题和摘要文本</h3><figure class="highlight html"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div><div class="line">17</div><div class="line">18</div><div class="line">19</div><div class="line">20</div><div class="line">21</div><div class="line">22</div><div class="line">23</div><div class="line">24</div><div class="line">25</div><div class="line">26</div><div class="line">27</div><div class="line">28</div><div class="line">29</div><div class="line">30</div><div 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class="line">403</div></pre></td><td class="code"><pre><div class="line"><?xml version="1.0" encoding="utf-8"?></div><div class="line"><span class="meta"><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"></span></div><div class="line"><span class="tag"><<span class="name">html</span> <span class="attr">xmlns</span>=<span class="string">"http://www.w3.org/1999/xhtml"</span>></span></div><div class="line"> <span class="tag"><<span class="name">head</span> <span class="attr">xmlns:xi</span>=<span class="string">"http://www.w3.org/2001/XInclude"</span>></span><span class="tag"><<span class="name">meta</span> <span class="attr">http-equiv</span>=<span class="string">"Content-Type"</span> <span class="attr">content</span>=<span class="string">"text/html; charset=utf-8"</span> /></span></div><div class="line"> <span class="comment"><!-- meta --></span></div><div class="line"> <span class="tag"><<span 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class="string">"http://blast.ncbi.nlm.nih.gov"</span> <span class="attr">title</span>=<span class="string">" Tool for finding local regions of sequence similarity "</span>></span>BLAST (Basic Local Alignment Search Tool)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download"</span> <span class="attr">title</span>=<span class="string">" BLAST programs for a local computer "</span>></span>BLAST (Stand-alone)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Structure/CN3D/cn3d.shtml"</span> <span class="attr">title</span>=<span class="string">" Program for viewing 3D structures and alignments "</span>></span>Cn3D<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Structure/cdd/wrpsb.cgi"</span> <span class="attr">title</span>=<span class="string">" Locates conserved domains within a protein sequence "</span>></span>Conserved Domain Search Service (CD Search)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK25501/ "</span> <span class="attr">title</span>=<span class="string">" URL application programming interface for searching, linking and downloading data within NCBI's Entrez system "</span>></span>E-Utilities<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/WebSub/?tool=genbank"</span> <span class="attr">title</span>=<span class="string">" Web tool for simple submissions of nucleotide sequences "</span>></span>GenBank: BankIt<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/projects/Sequin"</span> <span class="attr">title</span>=<span class="string">" Software tool for complex submissions of nucleotide sequences "</span>></span>GenBank: Sequin<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/genbank/tbl2asn2.html"</span> <span class="attr">title</span>=<span class="string">" Command-line program for submitting sequence data "</span>></span>GenBank: tbl2asn<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/protmap.cgi"</span> <span class="attr">title</span>=<span class="string">" Maps proteins from a COG/VOG back to its genome "</span>></span>Genome ProtMap<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/projects/gbench/"</span> <span class="attr">title</span>=<span class="string">" Stand-alone application for analyzing sequence data "</span>></span>Genome Workbench<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/tools/primer-blast"</span> <span class="attr">title</span>=<span class="string">" Designs PCR primers and analyzes them for target specificity using BLAST. "</span>></span>Primer-BLAST<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/static/prosplign/prosplign.html"</span> <span class="attr">title</span>=<span class="string">" Tool for aligning proteins to genomic DNA "</span>></span>ProSplign<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"http://pubchem.ncbi.nlm.nih.gov/search/search.cgi"</span> <span class="attr">title</span>=<span class="string">" Searches PubChem Compound by chemical structure "</span>></span>PubChem Structure Search<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"http://www.ncbi.nlm.nih.gov/projects/SNP"</span> <span class="attr">title</span>=<span class="string">" The SNP database tools page provides links to the general submission guidelines and to the submission handle request. "</span>></span>SNP Submission Tool<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/splign"</span> <span class="attr">title</span>=<span class="string">" Tool for aligning transcripts to genomic DNA "</span>></span>Splign<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Structure/VAST/vast.html"</span> <span class="attr">title</span>=<span class="string">" Tool that generates 3D structural alignments "</span>></span>Vector Alignment Search Tool (VAST)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/data-software/"</span>></span>All Data &amp; Software Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#domains-structures"</span>></span>Domains &amp; Structures<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu domains-structures"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/biosystems/"</span> <span class="attr">title</span>=<span class="string">" Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships. "</span>></span>BioSystems<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Structure/CN3D/cn3d.shtml"</span> <span class="attr">title</span>=<span class="string">" Program for viewing 3D structures and alignments "</span>></span>Cn3D<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/cdd"</span> <span class="attr">title</span>=<span class="string">" Database of conserved protein domains represented by multiple sequence alignments "</span>></span>Conserved Domain Database (CDD)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Structure/cdd/wrpsb.cgi"</span> <span class="attr">title</span>=<span class="string">" Locates conserved domains within a protein sequence "</span>></span>Conserved Domain Search Service (CD Search)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sites/entrez?db=structure"</span> <span class="attr">title</span>=<span class="string">" Database of 3D macromolecular structures derived from PDB "</span>></span>Structure (Molecular Modeling Database)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Structure/VAST/vast.html"</span> <span class="attr">title</span>=<span class="string">" Tool that generates 3D structural alignments "</span>></span>Vector Alignment Search Tool (VAST)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/domains-structures/"</span>></span>All Domains &amp; Structures Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#genes-expression"</span>></span>Genes &amp; Expression<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu genes-expression"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/biosystems/"</span> <span class="attr">title</span>=<span class="string">" Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships. "</span>></span>BioSystems<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/gap"</span> <span class="attr">title</span>=<span class="string">" Genotype/Phenotype association studies "</span>></span>Database of Genotypes and Phenotypes (dbGaP)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK25501/ "</span> <span class="attr">title</span>=<span class="string">" URL application programming interface for searching, linking and downloading data within NCBI's Entrez system "</span>></span>E-Utilities<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/gene"</span> <span class="attr">title</span>=<span class="string">" Database of gene loci and associated transcripts and proteins "</span>></span>Gene<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/geo/"</span> <span class="attr">title</span>=<span class="string">" Gene Expression Omnibus (GEO) Database "</span>></span>Gene Expression Omnibus (GEO) Database <span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/gds"</span> <span class="attr">title</span>=<span class="string">" Curated collections of gene expression data sets "</span>></span>Gene Expression Omnibus (GEO) Datasets<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/geoprofiles/"</span> <span class="attr">title</span>=<span class="string">" Database of gene expression Profiles for individual sequences "</span>></span>Gene Expression Omnibus (GEO) Profiles<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/projects/gbench/"</span> <span class="attr">title</span>=<span class="string">" Stand-alone application for analyzing sequence data "</span>></span>Genome Workbench<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/homologene"</span> <span class="attr">title</span>=<span class="string">" Sets of homologous eukaryotic genes "</span>></span>HomoloGene<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/mapview/"</span> <span class="attr">title</span>=<span class="string">" Tool for searching, viewing and downloading genomic maps and related data "</span>></span>Map Viewer<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/omim"</span> <span class="attr">title</span>=<span class="string">" Database of human genes and genetic disorders "</span>></span>Online Mendelian Inheritance in Man (OMIM)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/refseq/rsg/"</span> <span class="attr">title</span>=<span class="string">" RefSeqGene reference standards for genomic sequences of well-characterized genes "</span>></span>RefSeqGene<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/unigene"</span> <span class="attr">title</span>=<span class="string">" Gene-centered clusters of transcripts and ESTs "</span>></span>UniGene<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/genes-expression/"</span>></span>All Genes &amp; Expression Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#genetics-medicine"</span>></span>Genetics &amp; Medicine<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu genetics-medicine"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books"</span> <span class="attr">title</span>=<span class="string">" Online biomedical books "</span>></span>Bookshelf<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/gap"</span> <span class="attr">title</span>=<span class="string">" Genotype/Phenotype association studies "</span>></span>Database of Genotypes and Phenotypes (dbGaP)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/gtr/"</span> <span class="attr">title</span>=<span class="string">" Detailed information about genetic tests and labs "</span>></span>Genetic Testing Registry<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/genomes/FLU/"</span> <span class="attr">title</span>=<span class="string">" Data from the NIAID Influenza Genome Sequencing Project "</span>></span>Influenza Virus<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/mapview/"</span> <span class="attr">title</span>=<span class="string">" Tool for searching, viewing and downloading genomic maps and related data "</span>></span>Map Viewer<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/omim"</span> <span class="attr">title</span>=<span class="string">" Database of human genes and genetic disorders "</span>></span>Online Mendelian Inheritance in Man (OMIM)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed"</span> <span class="attr">title</span>=<span class="string">" Biomedical literature abstracts "</span>></span>PubMed<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pmc/"</span> <span class="attr">title</span>=<span class="string">" Free, full-text articles "</span>></span>PubMed Central (PMC)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed/clinical "</span> <span class="attr">title</span>=<span class="string">" Directory of PubMed queries about clinical topics "</span>></span>PubMed Clinical Queries<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/refseq/rsg/"</span> <span class="attr">title</span>=<span class="string">" RefSeqGene reference standards for genomic sequences of well-characterized genes "</span>></span>RefSeqGene<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/genetics-medicine/"</span>></span>All Genetics &amp; Medicine Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#genomes-maps"</span>></span>Genomes &amp; Maps<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu genomes-maps"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/dbvar"</span> <span class="attr">title</span>=<span class="string">" A database of genomic structural variation "</span>></span>Database of Genomic Structural Variation (dbVar)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/genbank/tbl2asn2.html"</span> <span class="attr">title</span>=<span class="string">" Command-line program for submitting sequence data "</span>></span>GenBank: tbl2asn<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sites/genome"</span> <span class="attr">title</span>=<span class="string">" Curated genomic DNA sequences "</span>></span>Genome<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/genomeprj"</span> <span class="attr">title</span>=<span class="string">" Central status pages for genome sequencing projects "</span>></span>Genome Project<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/protmap.cgi"</span> <span class="attr">title</span>=<span class="string">" Maps proteins from a COG/VOG back to its genome "</span>></span>Genome ProtMap<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/projects/gbench/"</span> <span class="attr">title</span>=<span class="string">" Stand-alone application for analyzing sequence data "</span>></span>Genome Workbench<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/genomes/FLU/"</span> <span class="attr">title</span>=<span class="string">" Data from the NIAID Influenza Genome Sequencing Project "</span>></span>Influenza Virus<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/mapview/"</span> <span class="attr">title</span>=<span class="string">" Tool for searching, viewing and downloading genomic maps and related data "</span>></span>Map Viewer<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/nuccore"</span> <span class="attr">title</span>=<span class="string">" Nucleotide sequence data in GenBank and RefSeq "</span>></span>Nucleotide Database<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/popset"</span> <span class="attr">title</span>=<span class="string">" Sets of nucleotide sequences representing a population "</span>></span>PopSet<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/static/prosplign/prosplign.html"</span> <span class="attr">title</span>=<span class="string">" Tool for aligning proteins to genomic DNA "</span>></span>ProSplign<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Traces/sra/sra.cgi?"</span> <span class="attr">title</span>=<span class="string">" Database of sequences reads from next generation sequencing technologies "</span>></span>Sequence Read Archive (SRA)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/splign"</span> <span class="attr">title</span>=<span class="string">" Tool for aligning transcripts to genomic DNA "</span>></span>Splign<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Traces/trace.cgi"</span> <span class="attr">title</span>=<span class="string">" DNA chromatograms, base calls, and quality estimates for single-pass reads. "</span>></span>Trace Archive<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/unists"</span> <span class="attr">title</span>=<span class="string">" Database of Sequence Tagged Sites "</span>></span>UniSTS<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/genomes-maps/"</span>></span>All Genomes &amp; Maps Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#homology"</span>></span>Homology<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu homology"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"http://blast.ncbi.nlm.nih.gov"</span> <span class="attr">title</span>=<span class="string">" Tool for finding local regions of sequence similarity "</span>></span>BLAST (Basic Local Alignment Search Tool)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download"</span> <span class="attr">title</span>=<span class="string">" BLAST programs for a local computer "</span>></span>BLAST (Stand-alone)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/blink.cgi?mode=query"</span> <span class="attr">title</span>=<span class="string">" Pre-computed reports showing proteins with similar sequences "</span>></span>BLAST Link (BLink)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/cdd"</span> <span class="attr">title</span>=<span class="string">" Database of conserved protein domains represented by multiple sequence alignments "</span>></span>Conserved Domain Database (CDD)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Structure/cdd/wrpsb.cgi"</span> <span class="attr">title</span>=<span class="string">" Locates conserved domains within a protein sequence "</span>></span>Conserved Domain Search Service (CD Search)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/protmap.cgi"</span> <span class="attr">title</span>=<span class="string">" Maps proteins from a COG/VOG back to its genome "</span>></span>Genome ProtMap<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/homologene"</span> <span class="attr">title</span>=<span class="string">" Sets of homologous eukaryotic genes "</span>></span>HomoloGene<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/proteinclusters"</span> <span class="attr">title</span>=<span class="string">" Clusters of related proteins from prokaryotes and organelles "</span>></span>Protein Clusters<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/homology/"</span>></span>All Homology Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#literature"</span>></span>Literature<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu literature"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books"</span> <span class="attr">title</span>=<span class="string">" Online biomedical books "</span>></span>Bookshelf<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK25501/ "</span> <span class="attr">title</span>=<span class="string">" URL application programming interface for searching, linking and downloading data within NCBI's Entrez system "</span>></span>E-Utilities<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/nlmcatalog/journals"</span> <span class="attr">title</span>=<span class="string">" Information on journals cited by NCBI records "</span>></span>Journals in NCBI Databases<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/mesh"</span> <span class="attr">title</span>=<span class="string">" Controlled vocabulary for MEDLINE "</span>></span>MeSH Database<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK21101/"</span> <span class="attr">title</span>=<span class="string">" Introductory articles about NCBI resources "</span>></span>NCBI Handbook<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK3831/"</span> <span class="attr">title</span>=<span class="string">" Online, searchable help documentation "</span>></span>NCBI Help Manual<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK1969/"</span> <span class="attr">title</span>=<span class="string">" NCBI's monthly newsletter "</span>></span>NCBI News<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed"</span> <span class="attr">title</span>=<span class="string">" Biomedical literature abstracts "</span>></span>PubMed<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pmc/"</span> <span class="attr">title</span>=<span class="string">" Free, full-text articles "</span>></span>PubMed Central (PMC)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed/clinical "</span> <span class="attr">title</span>=<span class="string">" Directory of PubMed queries about clinical topics "</span>></span>PubMed Clinical Queries<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmedhealth"</span> <span class="attr">title</span>=<span class="string">" Reviews of clinical effectiveness research "</span>></span>PubMed Health<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/literature/"</span>></span>All Literature Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#proteins"</span>></span>Proteins<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu proteins"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/biosystems/"</span> <span class="attr">title</span>=<span class="string">" Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships. "</span>></span>BioSystems<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"http://blast.ncbi.nlm.nih.gov"</span> <span class="attr">title</span>=<span class="string">" Tool for finding local regions of sequence similarity "</span>></span>BLAST (Basic Local Alignment Search Tool)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download"</span> <span class="attr">title</span>=<span class="string">" BLAST programs for a local computer "</span>></span>BLAST (Stand-alone)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/blink.cgi?mode=query"</span> <span class="attr">title</span>=<span class="string">" Pre-computed reports showing proteins with similar sequences "</span>></span>BLAST Link (BLink)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/cdd"</span> <span class="attr">title</span>=<span class="string">" Database of conserved protein domains represented by multiple sequence alignments "</span>></span>Conserved Domain Database (CDD)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Structure/cdd/wrpsb.cgi"</span> <span class="attr">title</span>=<span class="string">" Locates conserved domains within a protein sequence "</span>></span>Conserved Domain Search Service (CD Search)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK25501/ "</span> <span class="attr">title</span>=<span class="string">" URL application programming interface for searching, linking and downloading data within NCBI's Entrez system "</span>></span>E-Utilities<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/static/prosplign/prosplign.html"</span> <span class="attr">title</span>=<span class="string">" Tool for aligning proteins to genomic DNA "</span>></span>ProSplign<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/proteinclusters"</span> <span class="attr">title</span>=<span class="string">" Clusters of related proteins from prokaryotes and organelles "</span>></span>Protein Clusters<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/protein"</span> <span class="attr">title</span>=<span class="string">" Protein sequence data "</span>></span>Protein Database<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/RefSeq/"</span> <span class="attr">title</span>=<span class="string">" Curated nucleotide and protein sequences produced by NCBI "</span>></span>Reference Sequence (RefSeq)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/proteins/"</span>></span>All Proteins Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#sequence-analysis"</span>></span>Sequence Analysis<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu sequence-analysis"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"http://blast.ncbi.nlm.nih.gov"</span> <span class="attr">title</span>=<span class="string">" Tool for finding local regions of sequence similarity "</span>></span>BLAST (Basic Local Alignment Search Tool)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download"</span> <span class="attr">title</span>=<span class="string">" BLAST programs for a local computer "</span>></span>BLAST (Stand-alone)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/blink.cgi?mode=query"</span> <span class="attr">title</span>=<span class="string">" Pre-computed reports showing proteins with similar sequences "</span>></span>BLAST Link (BLink)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Structure/cdd/wrpsb.cgi"</span> <span class="attr">title</span>=<span class="string">" Locates conserved domains within a protein sequence "</span>></span>Conserved Domain Search Service (CD Search)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/protmap.cgi"</span> <span class="attr">title</span>=<span class="string">" Maps proteins from a COG/VOG back to its genome "</span>></span>Genome ProtMap<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/projects/gbench/"</span> <span class="attr">title</span>=<span class="string">" Stand-alone application for analyzing sequence data "</span>></span>Genome Workbench<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/genomes/FLU/"</span> <span class="attr">title</span>=<span class="string">" Data from the NIAID Influenza Genome Sequencing Project "</span>></span>Influenza Virus<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/tools/primer-blast"</span> <span class="attr">title</span>=<span class="string">" Designs PCR primers and analyzes them for target specificity using BLAST. "</span>></span>Primer-BLAST<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/static/prosplign/prosplign.html"</span> <span class="attr">title</span>=<span class="string">" Tool for aligning proteins to genomic DNA "</span>></span>ProSplign<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/sutils/splign"</span> <span class="attr">title</span>=<span class="string">" Tool for aligning transcripts to genomic DNA "</span>></span>Splign<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/sequence-analysis/"</span>></span>All Sequence Analysis Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#taxonomy"</span>></span>Taxonomy<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu taxonomy"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/taxonomy"</span> <span class="attr">title</span>=<span class="string">" The NCBI taxonomy tree in Entrez "</span>></span>Taxonomy<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Taxonomy/Browser/wwwtax.cgi?mode=Root"</span> <span class="attr">title</span>=<span class="string">" Displays and links Entrez data to each taxonomic node "</span>></span>Taxonomy Browser<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/Taxonomy/CommonTree/wwwcmt.cgi"</span> <span class="attr">title</span>=<span class="string">" Creates custom taxonomic trees "</span>></span>Taxonomy Common Tree<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/taxonomy/"</span>></span>All Taxonomy Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#training-tutorials"</span>></span>Training &amp; Tutorials<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu training-tutorials"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/education/"</span> <span class="attr">title</span>=<span class="string">" Central page providing links to tutorials and training materials "</span>></span>NCBI Education Page<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK21101/"</span> <span class="attr">title</span>=<span class="string">" Introductory articles about NCBI resources "</span>></span>NCBI Handbook<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK3831/"</span> <span class="attr">title</span>=<span class="string">" Online, searchable help documentation "</span>></span>NCBI Help Manual<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK1969/"</span> <span class="attr">title</span>=<span class="string">" NCBI's monthly newsletter "</span>></span>NCBI News<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/About/primer/"</span> <span class="attr">title</span>=<span class="string">" An introduction to bioinformatics at NCBI "</span>></span>Science Primer<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/training-tutorials/"</span>></span>All Training &amp; Tutorials Resources...<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#variation"</span>></span>Variation<span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"actual-resources-submenu variation"</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/dbvar"</span> <span class="attr">title</span>=<span class="string">" A database of genomic structural variation "</span>></span>Database of Genomic Structural Variation (dbVar)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/gap"</span> <span class="attr">title</span>=<span class="string">" Genotype/Phenotype association studies "</span>></span>Database of Genotypes and Phenotypes (dbGaP)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/snp"</span> <span class="attr">title</span>=<span class="string">" Database of nucleotide sequence polymorphisms "</span>></span>Database of Single Nucleotide Polymorphisms (dbSNP)<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"http://www.ncbi.nlm.nih.gov/projects/SNP"</span> <span class="attr">title</span>=<span class="string">" The SNP database tools page provides links to the general submission guidelines and to the submission handle request. 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class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/homology/#howtos"</span>></span>Homology<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/literature/#howtos"</span>></span>Literature<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/guide/proteins/#howtos"</span>></span>Proteins<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span 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class="name">div</span> <span class="attr">class</span>=<span class="string">"search"</span>></span><span class="tag"><<span class="name">label</span> <span class="attr">for</span>=<span class="string">"search_term"</span> <span class="attr">class</span>=<span class="string">"offscreen_noflow"</span>></span>Search term<span class="tag"></<span class="name">label</span>></span><span class="tag"><<span class="name">label</span> <span class="attr">for</span>=<span class="string">"database"</span> <span class="attr">class</span>=<span class="string">"offscreen_noflow"</span>></span>Search database<span class="tag"></<span class="name">label</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"search_form"</span>></span><span class="tag"><<span class="name">select</span> <span class="attr">name</span>=<span class="string">"EntrezSystem2.PEntrez.PubMed.Pubmed_SearchBar.SearchResourceList"</span> <span class="attr">sid</span>=<span class="string">"1"</span> <span class="attr">id</span>=<span class="string">"database"</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/sites/gquery"</span> <span class="attr">resource</span>=<span class="string">"gquery"</span>></span>All Databases<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">selected</span>=<span class="string">"selected"</span> <span class="attr">value</span>=<span class="string">"pubmed"</span> <span class="attr">resource</span>=<span class="string">"pubmed"</span>></span>PubMed<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/protein"</span> <span class="attr">resource</span>=<span class="string">"protein"</span>></span>Protein<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/nuccore"</span> <span class="attr">resource</span>=<span class="string">"nuccore"</span>></span>Nucleotide<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/nucgss"</span> <span class="attr">resource</span>=<span class="string">"nucgss"</span>></span>GSS<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/nucest"</span> <span class="attr">resource</span>=<span class="string">"nucest"</span>></span>EST<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/structure"</span> <span class="attr">resource</span>=<span class="string">"structure"</span>></span>Structure<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/genome"</span> <span class="attr">resource</span>=<span class="string">"genome"</span>></span>Genome<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/assembly"</span> <span class="attr">resource</span>=<span class="string">"assembly"</span>></span>Assembly<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/bioproject"</span> <span class="attr">resource</span>=<span class="string">"bioproject"</span>></span>BioProject<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/biosample"</span> <span class="attr">resource</span>=<span class="string">"biosample"</span>></span>BioSample<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/biosystems"</span> <span class="attr">resource</span>=<span class="string">"biosystems"</span>></span>BioSystems<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/books"</span> <span class="attr">resource</span>=<span class="string">"books"</span>></span>Books<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/cdd"</span> <span class="attr">resource</span>=<span class="string">"cdd"</span>></span>Conserved Domains<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/clone"</span> <span class="attr">resource</span>=<span class="string">"clone"</span>></span>Clone<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/gap"</span> <span class="attr">resource</span>=<span class="string">"gap"</span>></span>dbGaP<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/dbvar"</span> <span class="attr">resource</span>=<span class="string">"dbvar"</span>></span>dbVar<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/epigenomics"</span> <span class="attr">resource</span>=<span class="string">"epigenomics"</span>></span>Epigenomics<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/gene"</span> <span class="attr">resource</span>=<span class="string">"gene"</span>></span>Gene<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/gds"</span> <span class="attr">resource</span>=<span class="string">"gds"</span>></span>GEO DataSets<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/geoprofiles"</span> <span class="attr">resource</span>=<span class="string">"geoprofiles"</span>></span>GEO Profiles<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/homologene"</span> <span class="attr">resource</span>=<span class="string">"homologene"</span>></span>HomoloGene<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/medgen"</span> <span class="attr">resource</span>=<span class="string">"medgen"</span>></span>MedGen<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/mesh"</span> <span class="attr">resource</span>=<span class="string">"mesh"</span>></span>MeSH<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/ncbisearch"</span> <span class="attr">resource</span>=<span class="string">"ncbisearch"</span>></span>NCBI Web Site<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/nlmcatalog"</span> <span class="attr">resource</span>=<span class="string">"nlmcatalog"</span>></span>NLM Catalog<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/omia"</span> <span class="attr">resource</span>=<span class="string">"omia"</span>></span>OMIA<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/omim"</span> <span class="attr">resource</span>=<span class="string">"omim"</span>></span>OMIM<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/pmc"</span> <span class="attr">resource</span>=<span class="string">"pmc"</span>></span>PMC<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/popset"</span> <span class="attr">resource</span>=<span class="string">"popset"</span>></span>PopSet<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/probe"</span> <span class="attr">resource</span>=<span class="string">"probe"</span>></span>Probe<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/proteinclusters"</span> <span class="attr">resource</span>=<span class="string">"proteinclusters"</span>></span>Protein Clusters<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/pcassay"</span> <span class="attr">resource</span>=<span class="string">"pcassay"</span>></span>PubChem BioAssay<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/pccompound"</span> <span class="attr">resource</span>=<span class="string">"pccompound"</span>></span>PubChem Compound<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/pcsubstance"</span> <span class="attr">resource</span>=<span class="string">"pcsubstance"</span>></span>PubChem Substance<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span class="name">option</span> <span class="attr">value</span>=<span class="string">"/pubmedhealth"</span> <span class="attr">resource</span>=<span 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class="attr">value</span>=<span class="string">"18235848[uid]"</span> <span class="attr">title</span>=<span class="string">"Search PubMed"</span> <span class="attr">cmd</span>=<span class="string">"Go"</span> <span class="attr">pg</span>=<span class="string">"results"</span> <span class="attr">class</span>=<span class="string">"jig-ncbiautofocus jig-ncbiclearbutton jig-ncbiautocomplete"</span> <span class="attr">config</span>=<span class="string">"dictionary:'pm_related_queries_2',disableUrl:'EntrezSearchBarAutoComplCtrl'"</span> <span class="attr">autocomplete</span>=<span class="string">"off"</span> <span class="attr">suggest</span>=<span class="string">"true"</span> /></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">button</span> <span class="attr">name</span>=<span class="string">"EntrezSystem2.PEntrez.PubMed.Pubmed_SearchBar.Search"</span> <span class="attr">sid</span>=<span class="string">"1"</span> <span class="attr">id</span>=<span class="string">"search"</span> <span class="attr">class</span>=<span class="string">"button_search nowrap"</span> <span class="attr">cmd</span>=<span class="string">"go"</span>></span>Search<span class="tag"></<span class="name">button</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">ul</span> <span class="attr">class</span>=<span class="string">"searchlinks inline_list"</span>></span><span class="tag"><<span class="name">li</span> <span class="attr">id</span>=<span class="string">"rss_dropdown"</span> <span class="attr">class</span>=<span class="string">"jig-ncbipopper"</span> <span class="attr">config</span>=<span class="string">"targetPosition : 'bottom center',sourcePosition : 'top center',sourceSelector : '#rss_menu', hasArrow : false,openMethod : 'click',closeMethod : 'click',isSourceElementCloseClick: false, groupName: 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NCBI"</span> <span class="attr">href</span>=<span class="string">"/sites/myncbi/searches/save?db=pubmed&amp;qk=1"</span> <span class="attr">id</span>=<span class="string">"SaveSearch"</span>></span>Save search<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">name</span>=<span class="string">"EntrezSystem2.PEntrez.PubMed.Pubmed_SearchBar.Advanced"</span> <span class="attr">sid</span>=<span class="string">"1"</span> <span class="attr">href</span>=<span class="string">"/pubmed/advanced"</span> <span class="attr">id</span>=<span class="string">"EntrezSystem2.PEntrez.PubMed.Pubmed_SearchBar.Advanced"</span>></span>Advanced<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span> <span class="attr">class</span>=<span class="string">"help"</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/books/NBK3827/"</span> <span class="attr">name</span>=<span class="string">"help"</span> <span class="attr">target</span>=<span class="string">"_blank"</span> <span class="attr">id</span>=<span class="string">"help"</span>></span>Help<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">id</span>=<span class="string">"rss_menu"</span> <span class="attr">class</span>=<span class="string">"rss_menu tabPopper"</span>></span><span class="tag"><<span class="name">fieldset</span>></span><span class="tag"><<span class="name">legend</span>></span>RSS Settings<span class="tag"></<span class="name">legend</span>></span><span class="tag"><<span class="name">ul</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">span</span>></span>Search: <span class="tag"></<span class="name">span</span>></span>18235848[uid]<span class="tag"></<span class="name">li</span>></span><span class="tag"><<span class="name">li</span>></span><span class="tag"><<span class="name">label</span> <span class="attr">for</span>=<span class="string">"rss_results"</span>></span>Number of items displayed:<span class="tag"></<span class="name">label</span>></span><span class="tag"><<span class="name">select</span> <span class="attr">name</span>=<span class="string">"EntrezSystem2.PEntrez.PubMed.Pubmed_SearchBar.FeedLimit"</span> <span class="attr">sid</span>=<span class="string">"1"</span> <span class="attr">id</span>=<span class="string">"rss_results"</span>></span><span class="tag"><<span class="name">option</span>></span>5<span class="tag"></<span class="name">option</span>></span><span class="tag"><<span 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class="name">label</span>></span><span class="tag"><<span class="name">input</span> <span class="attr">name</span>=<span class="string">"EntrezSystem2.PEntrez.PubMed.Pubmed_SearchBar.FeedName"</span> <span class="attr">sid</span>=<span class="string">"1"</span> <span class="attr">type</span>=<span class="string">"text"</span> <span class="attr">id</span>=<span class="string">"rss_name"</span> <span class="attr">value</span>=<span class="string">"18235848[uid]"</span> <span class="attr">size</span>=<span class="string">"30"</span> /></span><span class="tag"></<span class="name">li</span>></span><span class="tag"></<span class="name">ul</span>></span><span class="tag"><<span class="name">button</span> <span class="attr">class</span>=<span class="string">"button_apply"</span> <span class="attr">type</span>=<span class="string">"submit"</span> <span class="attr">sid</span>=<span class="string">"1"</span> <span class="attr">name</span>=<span class="string">"EntrezSystem2.PEntrez.PubMed.Pubmed_SearchBar.CreateRssFeed"</span> <span class="attr">id</span>=<span class="string">"rss_createfeed"</span> <span class="attr">qk</span>=<span class="string">"1"</span> <span class="attr">hid</span>=<span class="string">"1FUNJN4PV2T7eEBE-2QXO_HGHiXQ3KJETB4YG2_a1FIOHYssJDK72SGp31FyiE1Q2USxFGNjYm4DBvmWwokuCpCCLROe-BPZRbU"</span>></span>Create RSS<span class="tag"></<span class="name">button</span>></span><span class="tag"></<span class="name">fieldset</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">input</span> <span class="attr">name</span>=<span class="string">"EntrezSystem2.PEntrez.PubMed.Pubmed_SearchBar.CurrDb"</span> <span class="attr">sid</span>=<span class="string">"1"</span> <span class="attr">type</span>=<span class="string">"hidden"</span> <span class="attr">value</span>=<span class="string">"pubmed"</span> /></span><span class="tag"></<span class="name">div</span>></span></div><div class="line"><span class="tag"></<span class="name">div</span>></span> </div><div class="line"> <span class="tag"><<span class="name">input</span> <span class="attr">name</span>=<span class="string">"EntrezSystem2.PEntrez.PubMed.Pubmed_PageController.PreviousPageName"</span> <span class="attr">sid</span>=<span class="string">"1"</span> <span class="attr">type</span>=<span class="string">"hidden"</span> <span class="attr">value</span>=<span class="string">"results"</span> /></span></div><div class="line"> <span class="tag"><<span class="name">div</span> <span class="attr">id</span>=<span class="string">"faceted_search"</span> <span class="attr">class</span>=<span class="string">""</span>></span></div><div class="line"> <span class="tag"><<span class="name">h2</span> <span class="attr">class</span>=<span class="string">"offscreen_noflow"</span>></span>Result Filters<span class="tag"></<span class="name">h2</span>></span></div><div class="line"> </div><div class="line"><span class="tag"></<span class="name">div</span>></span></div><div class="line"><span class="tag"><<span class="name">div</span> <span class="attr">id</span>=<span class="string">"maincontent"</span> <span class="attr">class</span>=<span class="string">"col nine_col"</span>></span></div><div class="line"> <span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"content"</span>></span></div><div class="line"> <span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"results_settings one_setting"</span>></span><span class="tag"><<span class="name">h4</span> <span class="attr">class</span>=<span class="string">"left display_settings content_header jig-ncbipopper"</span> <span class="attr">id</span>=<span class="string">"display_set"</span> <span class="attr">data-jigconfig</span>=<span class="string">"triggerPosition : 'bottom center',destPosition : 'top center',destSelector 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<span class="attr">name</span>=<span class="string">"EntrezSystem2.PEntrez.PubMed.Pubmed_ResultsPanel.Pubmed_ResultsController.RunLastQuery"</span> <span class="attr">sid</span>=<span class="string">"1"</span> <span class="attr">type</span>=<span class="string">"hidden"</span> /></span><span class="tag"></<span class="name">div</span>></span></div><div class="line"> </div><div class="line"> <span class="tag"></<span class="name">div</span>></span></div><div class="line"> <span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"rprt_all"</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"rprt abstract"</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"cit"</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"#"</span> <span class="attr">title</span>=<span class="string">"PLoS neglected tropical diseases."</span> <span class="attr">abstractLink</span>=<span class="string">"yes"</span> <span class="attr">alsec</span>=<span class="string">"jour"</span> <span class="attr">alterm</span>=<span class="string">"PLoS Negl Trop Dis."</span>></span>PLoS Negl Trop Dis.<span class="tag"></<span class="name">a</span>></span> 2008 Jan 2;2(1):e127. doi: 10.1371/journal.pntd.0000127.<span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">h1</span>></span>Quantitative high-throughput screen identifies inhibitors of the Schistosoma mansoni redox cascade.<span class="tag"></<span class="name">h1</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"auths"</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed?term=Simeonov%20A%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=18235848"</span>></span>Simeonov A<span class="tag"></<span class="name">a</span>></span>, <span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed?term=Jadhav%20A%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=18235848"</span>></span>Jadhav A<span class="tag"></<span class="name">a</span>></span>, <span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed?term=Sayed%20AA%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=18235848"</span>></span>Sayed AA<span class="tag"></<span class="name">a</span>></span>, <span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed?term=Wang%20Y%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=18235848"</span>></span>Wang Y<span class="tag"></<span class="name">a</span>></span>, <span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed?term=Nelson%20ME%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=18235848"</span>></span>Nelson ME<span class="tag"></<span class="name">a</span>></span>, <span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed?term=Thomas%20CJ%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=18235848"</span>></span>Thomas CJ<span class="tag"></<span class="name">a</span>></span>, <span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed?term=Inglese%20J%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=18235848"</span>></span>Inglese J<span class="tag"></<span class="name">a</span>></span>, <span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed?term=Williams%20DL%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=18235848"</span>></span>Williams DL<span class="tag"></<span class="name">a</span>></span>, <span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pubmed?term=Austin%20CP%5BAuthor%5D&amp;cauthor=true&amp;cauthor_uid=18235848"</span>></span>Austin CP<span class="tag"></<span class="name">a</span>></span>.<span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"aff"</span>></span><span class="tag"><<span class="name">h3</span> <span class="attr">class</span>=<span class="string">"label"</span>></span>Source<span class="tag"></<span class="name">h3</span>></span><span class="tag"><<span class="name">p</span>></span>NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America.<span class="tag"></<span class="name">p</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"abstr"</span>></span><span class="tag"><<span class="name">h3</span>></span>Abstract<span class="tag"></<span class="name">h3</span>></span><span class="tag"><<span class="name">p</span>></span>Schistosomiasis is a tropical disease associated with high morbidity and mortality, currently affecting over 200 million people worldwide. Praziquantel is the only drug used to treat the disease, and with its increased use the probability of developing drug resistance has grown significantly. The Schistosoma parasites can survive for up to decades in the human host due in part to a unique set of antioxidant enzymes that continuously degrade the reactive oxygen species produced by the host's innate immune response. Two principal components of this defense system have been recently identified in S. mansoni as thioredoxin/glutathione reductase (TGR) and peroxiredoxin (Prx) and as such these enzymes present attractive new targets for anti-schistosomiasis drug development. Inhibition of TGR/Prx activity was screened in a dual-enzyme format with reducing equivalents being transferred from NADPH to glutathione via a TGR-catalyzed reaction and then to hydrogen peroxide via a Prx-catalyzed step. A fully automated quantitative high-throughput (qHTS) experiment was performed against a collection of 71,028 compounds tested as 7- to 15-point concentration series at 5 microL reaction volume in 1536-well plate format. In order to generate a robust data set and to minimize the effect of compound autofluorescence, apparent reaction rates derived from a kinetic read were utilized instead of end-point measurements. Actives identified from the screen, along with previously untested analogues, were subjected to confirmatory experiments using the screening assay and subsequently against the individual targets in secondary assays. Several novel active series were identified which inhibited TGR at a range of potencies, with IC(50)s ranging from micromolar to the assay response limit ( approximately 25 nM). This is, to our knowledge, the first report of a large-scale HTS to identify lead compounds for a helminthic disease, and provides a paradigm that can be used to jump-start development of novel therapeutics for other neglected tropical diseases.<span class="tag"></<span class="name">p</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"aux"</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"resc"</span>></span><span class="tag"><<span class="name">dl</span> <span class="attr">class</span>=<span class="string">"rprtid"</span>></span><span class="tag"><<span class="name">dt</span>></span>PMID:<span class="tag"></<span class="name">dt</span>></span> <span class="tag"><<span class="name">dd</span>></span><span class="tag"><<span class="name">span</span> <span class="attr">class</span>=<span 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class="string">"log$=imagestrip_free_text&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/"</span>></span> Free text<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">p</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"img_strip"</span>></span><span class="tag"><<span class="name">script</span> <span class="attr">type</span>=<span class="string">"text/javascript"</span>></span><span class="undefined"></span></div><div class="line"> var imageStripObj = {};</div><div class="line"> imageStripObj.images = [];</div><div class="line"> imageStripObj.start = 0;</div><div class="line"> imageStripObj.maxImagesPerView = 7;</div><div class="line"> imageStripObj.count = 5;</div><div class="line"> imageStripObj.containerSelector = ".pmc_images";</div><div class="line"> imageStripObj.CommonCitation = "PLoS Negl Trop Dis. 2008 January;2(1):e127.";</div><div class="line"> imageStripObj.ImageStripLogVal = "image_preview";</div><div class="line"> imageStripObj.ImageStripPreviewLogName = "previewimagepos";</div><div class="line"> <span class="tag"></<span class="name">script</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">class</span>=<span class="string">"img_strip_arrow img_strip_left_arrow posL"</span> <span class="attr">href</span>=<span class="string">""</span>></span><span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"img_strip_item_cont"</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"img_strip_item pos1"</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">class</span>=<span class="string">"figpopup"</span> <span class="attr">co-legend-rid</span>=<span class="string">"imgstrip_colegend1"</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/figure/pntd-0000127-g001/"</span> <span class="attr">image-pos</span>=<span class="string">"1"</span> <span class="attr">ref</span>=<span class="string">"log$=image_preview&amp;previewimagepos=1&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span>></span><span class="tag"><<span class="name">img</span> <span class="attr">src</span>=<span class="string">"/pmc/articles/instance/2217675/bin/pntd.0000127.g001.gif"</span> <span class="attr">src-large</span>=<span class="string">"/pmc/articles/instance/2217675/bin/pntd.0000127.g001.jpg"</span> <span class="attr">alt</span>=<span class="string">"Figure 1"</span> /></span><span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">style</span>=<span class="string">"display:none"</span> <span class="attr">id</span>=<span class="string">"imgstrip_colegend1"</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"legend-from"</span>></span><span class="tag"><<span class="name">span</span> <span class="attr">class</span>=<span class="string">"legend-from-title"</span>></span>Figure 1<span class="tag"></<span class="name">span</span>></span><span class="tag"><<span class="name">div</span>></span>TGR/Prx2 assay principle.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"legend-citation"</span>></span><span class="tag"><<span class="name">div</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/"</span> <span class="attr">ref</span>=<span class="string">"log$=image_preview_title_link&amp;previewimagepos=1&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span>></span>Quantitative High-Throughput Screen Identifies Inhibitors of the Schistosoma mansoni Redox Cascade<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span>PLoS Negl Trop Dis. 2008 January;2(1):e127.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"img_strip_item pos2"</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">class</span>=<span class="string">"figpopup"</span> <span class="attr">co-legend-rid</span>=<span class="string">"imgstrip_colegend2"</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/figure/pntd-0000127-g002/"</span> <span class="attr">image-pos</span>=<span class="string">"2"</span> <span class="attr">ref</span>=<span class="string">"log$=image_preview&amp;previewimagepos=2&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span>></span><span class="tag"><<span class="name">img</span> <span class="attr">src</span>=<span class="string">"/pmc/articles/instance/2217675/bin/pntd.0000127.g002.gif"</span> <span class="attr">src-large</span>=<span class="string">"/pmc/articles/instance/2217675/bin/pntd.0000127.g002.jpg"</span> <span class="attr">alt</span>=<span class="string">"Figure 2"</span> /></span><span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">style</span>=<span class="string">"display:none"</span> <span class="attr">id</span>=<span class="string">"imgstrip_colegend2"</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"legend-from"</span>></span><span class="tag"><<span class="name">span</span> <span class="attr">class</span>=<span class="string">"legend-from-title"</span>></span>Figure 2<span class="tag"></<span class="name">span</span>></span><span class="tag"><<span class="name">div</span>></span>Screening reagents' stability as a function of storage time.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span>Bottles containing buffer, enzyme, and substrate stock solutions, respectively, were prepared and kept at 4°C. At the selected time points, the bottles were connected to a liquid dispenser and the assay was performed as described in Methods. Signal-to-background ratio (S∶B) and Z′ factor were computed as the average of 32 wells.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"legend-citation"</span>></span><span class="tag"><<span class="name">div</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/"</span> <span class="attr">ref</span>=<span class="string">"log$=image_preview_title_link&amp;previewimagepos=2&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span>></span>Quantitative High-Throughput Screen Identifies Inhibitors of the Schistosoma mansoni Redox Cascade<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span>PLoS Negl Trop Dis. 2008 January;2(1):e127.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"img_strip_item pos3"</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">class</span>=<span class="string">"figpopup"</span> <span class="attr">co-legend-rid</span>=<span class="string">"imgstrip_colegend3"</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/figure/pntd-0000127-g003/"</span> <span class="attr">image-pos</span>=<span class="string">"3"</span> <span class="attr">ref</span>=<span class="string">"log$=image_preview&amp;previewimagepos=3&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span>></span><span class="tag"><<span class="name">img</span> <span class="attr">src</span>=<span class="string">"/pmc/articles/instance/2217675/bin/pntd.0000127.g003.gif"</span> <span class="attr">src-large</span>=<span class="string">"/pmc/articles/instance/2217675/bin/pntd.0000127.g003.jpg"</span> <span class="attr">alt</span>=<span class="string">"Figure 3"</span> /></span><span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">style</span>=<span class="string">"display:none"</span> <span class="attr">id</span>=<span class="string">"imgstrip_colegend3"</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"legend-from"</span>></span><span class="tag"><<span class="name">span</span> <span class="attr">class</span>=<span class="string">"legend-from-title"</span>></span>Figure 3<span class="tag"></<span class="name">span</span>></span><span class="tag"><<span class="name">div</span>></span>qHTS performance.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span>Z′ trend (A) and intraplate control titrations (duplicate curves per plate) (B) as a function of plate number.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"legend-citation"</span>></span><span class="tag"><<span class="name">div</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/"</span> <span class="attr">ref</span>=<span class="string">"log$=image_preview_title_link&amp;previewimagepos=3&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span>></span>Quantitative High-Throughput Screen Identifies Inhibitors of the Schistosoma mansoni Redox Cascade<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span>PLoS Negl Trop Dis. 2008 January;2(1):e127.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"img_strip_item pos4"</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">class</span>=<span class="string">"figpopup"</span> <span class="attr">co-legend-rid</span>=<span class="string">"imgstrip_colegend4"</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/figure/pntd-0000127-g004/"</span> <span class="attr">image-pos</span>=<span class="string">"4"</span> <span class="attr">ref</span>=<span class="string">"log$=image_preview&amp;previewimagepos=4&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span>></span><span class="tag"><<span class="name">img</span> <span class="attr">src</span>=<span class="string">"/pmc/articles/instance/2217675/bin/pntd.0000127.g004.gif"</span> <span class="attr">src-large</span>=<span class="string">"/pmc/articles/instance/2217675/bin/pntd.0000127.g004.jpg"</span> <span class="attr">alt</span>=<span class="string">"Figure 4"</span> /></span><span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">style</span>=<span class="string">"display:none"</span> <span class="attr">id</span>=<span class="string">"imgstrip_colegend4"</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"legend-from"</span>></span><span class="tag"><<span class="name">span</span> <span class="attr">class</span>=<span class="string">"legend-from-title"</span>></span>Figure 4<span class="tag"></<span class="name">span</span>></span><span class="tag"><<span class="name">div</span>></span>Structure and potency (IC<span class="tag"><<span class="name">sub</span>></span>50<span class="tag"></<span class="name">sub</span>></span> in µM) of actives and series expansion analogues.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span>‘qHTS’ lists the IC<span class="tag"><<span class="name">sub</span>></span>50<span class="tag"></<span class="name">sub</span>></span> values obtained from the initial high throughput screen of the collection; ‘confirmation’ represents the IC<span class="tag"><<span class="name">sub</span>></span>50<span class="tag"></<span class="name">sub</span>></span> values obtained using the identical assay as in the qHTS from the compounds identified in qHTS and expansion series; ‘TGR Assay’ is the IC<span class="tag"><<span class="name">sub</span>></span>50<span class="tag"></<span class="name">sub</span>></span> values obtained in an assay of TGR activity using DTNB as a substrate. NS, not screened (compound not in the screening collection), ND, not determined, NA, not applicable. IC<span class="tag"><<span class="name">sub</span>></span>50<span class="tag"></<span class="name">sub</span>></span> values greater than 50 or 57 µM signify lack of fitted curve through the dose-response data, i.e. flat response within the range tested.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"legend-citation"</span>></span><span class="tag"><<span class="name">div</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/"</span> <span class="attr">ref</span>=<span class="string">"log$=image_preview_title_link&amp;previewimagepos=4&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span>></span>Quantitative High-Throughput Screen Identifies Inhibitors of the Schistosoma mansoni Redox Cascade<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span>PLoS Negl Trop Dis. 2008 January;2(1):e127.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"img_strip_item pos5"</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">class</span>=<span class="string">"figpopup"</span> <span class="attr">co-legend-rid</span>=<span class="string">"imgstrip_colegend5"</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/figure/pntd-0000127-g005/"</span> <span class="attr">image-pos</span>=<span class="string">"5"</span> <span class="attr">ref</span>=<span class="string">"log$=image_preview&amp;previewimagepos=5&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span>></span><span class="tag"><<span class="name">img</span> <span class="attr">src</span>=<span class="string">"/pmc/articles/instance/2217675/bin/pntd.0000127.g005.gif"</span> <span class="attr">src-large</span>=<span class="string">"/pmc/articles/instance/2217675/bin/pntd.0000127.g005.jpg"</span> <span class="attr">alt</span>=<span class="string">"Figure 5"</span> /></span><span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">style</span>=<span class="string">"display:none"</span> <span class="attr">id</span>=<span class="string">"imgstrip_colegend5"</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"legend-from"</span>></span><span class="tag"><<span class="name">span</span> <span class="attr">class</span>=<span class="string">"legend-from-title"</span>></span>Figure 5<span class="tag"></<span class="name">span</span>></span><span class="tag"><<span class="name">div</span>></span>Example time-course plots derived from the primary screen, followed to the right by the corresponding concentration-response curves.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span>(A, B) Non-fluorescent inhibitors, compounds 3 and 14; the decrease in fluorescence is inhibited at increasing compound concentrations while the starting fluorescence remains constant. (C) An example of an apparent activator (Ofloxacin): a highly fluorescent compound which appears to be reacting with one or more components of the assay. Four concentrations out of seven or fifteen are plotted in each of the time course plots for clarity; ▪, 3.2 nM; ▴, 16 nM; □, 10 µM; ▵, 50 µM.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span> <span class="attr">class</span>=<span class="string">"legend-citation"</span>></span><span class="tag"><<span class="name">div</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">href</span>=<span class="string">"/pmc/articles/PMC2217675/"</span> <span class="attr">ref</span>=<span class="string">"log$=image_preview_title_link&amp;previewimagepos=5&amp;ncbi_uid=18235848&amp;link_uid=PMC2217675"</span>></span>Quantitative High-Throughput Screen Identifies Inhibitors of the Schistosoma mansoni Redox Cascade<span class="tag"></<span class="name">a</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">div</span>></span>PLoS Negl Trop Dis. 2008 January;2(1):e127.<span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">a</span> <span class="attr">class</span>=<span class="string">"img_strip_arrow img_strip_arrow_right img_strip_right_arrow posR"</span> <span class="attr">href</span>=<span class="string">""</span>></span><span class="tag"></<span class="name">a</span>></span><span class="tag"><<span class="name">script</span> <span class="attr">type</span>=<span class="string">"text/javascript"</span>></span><span class="undefined"></span></div><div class="line"> imageStripObj.images[0]={</div><div class="line"> ImageUrl:"/pmc/articles/instance/2217675/bin/pntd.0000127.g001.jpg",</div><div class="line"> ImageSource:"/pmc/articles/PMC2217675/figure/pntd-0000127-g001/",</div><div class="line"> ThumbUrl:"/pmc/articles/instance/2217675/bin/pntd.0000127.g001.gif",</div><div class="line"> Label:"Figure%201",</div><div class="line"> SourceId:"/pmc/articles/PMC2217675/",</div><div class="line"> CaptionTitle:"TGR%2FPrx2%20assay%20principle.",</div><div class="line"> Caption:"",</div><div class="line"> ArticleTitle:"Quantitative%20High-Throughput%20Screen%20Identifies%20Inhibitors%20of%20the%20Schistosoma%20mansoni%20Redox%20Cascade",</div><div class="line"> ImagePosition:"1",</div><div class="line"> Citation:"PLoS Negl Trop Dis. 2008 January;2(1):e127.",</div><div class="line"> ncbi_uid:"18235848",</div><div class="line"> link_uid:"PMC2217675"</div><div class="line"> };</div><div class="line"> <span class="tag"></<span class="name">script</span>></span><span class="tag"><<span class="name">script</span> <span class="attr">type</span>=<span class="string">"text/javascript"</span>></span><span class="undefined"></span></div><div class="line"> imageStripObj.images[1]={</div><div class="line"> ImageUrl:"/pmc/articles/instance/2217675/bin/pntd.0000127.g002.jpg",</div><div class="line"> ImageSource:"/pmc/articles/PMC2217675/figure/pntd-0000127-g002/",</div><div class="line"> ThumbUrl:"/pmc/articles/instance/2217675/bin/pntd.0000127.g002.gif",</div><div class="line"> Label:"Figure%202",</div><div class="line"> SourceId:"/pmc/articles/PMC2217675/",</div><div class="line"> CaptionTitle:"Screening%20reagents'%20stability%20as%20a%20function%20of%20storage%20time.",</div><div class="line"> Caption:"Bottles containing buffer, enzyme, and substrate stock solutions, respectively, were prepared and kept at 4°C. At the selected time points, the bottles were connected to a liquid dispenser and the assay was performed as described in Methods. Signal-to-background ratio (S∶B) and Z′ factor were computed as the average of 32 wells.",</div><div class="line"> ArticleTitle:"Quantitative%20High-Throughput%20Screen%20Identifies%20Inhibitors%20of%20the%20Schistosoma%20mansoni%20Redox%20Cascade",</div><div class="line"> ImagePosition:"2",</div><div class="line"> Citation:"PLoS Negl Trop Dis. 2008 January;2(1):e127.",</div><div class="line"> ncbi_uid:"18235848",</div><div class="line"> link_uid:"PMC2217675"</div><div class="line"> };</div><div class="line"> <span class="tag"></<span class="name">script</span>></span><span class="tag"><<span class="name">script</span> <span class="attr">type</span>=<span class="string">"text/javascript"</span>></span><span class="undefined"></span></div><div class="line"> imageStripObj.images[2]={</div><div class="line"> ImageUrl:"/pmc/articles/instance/2217675/bin/pntd.0000127.g003.jpg",</div><div class="line"> ImageSource:"/pmc/articles/PMC2217675/figure/pntd-0000127-g003/",</div><div class="line"> ThumbUrl:"/pmc/articles/instance/2217675/bin/pntd.0000127.g003.gif",</div><div class="line"> Label:"Figure%203",</div><div class="line"> SourceId:"/pmc/articles/PMC2217675/",</div><div class="line"> CaptionTitle:"qHTS%20performance.",</div><div class="line"> Caption:"Z′ trend (A) and intraplate control titrations (duplicate curves per plate) (B) as a function of plate number.",</div><div class="line"> ArticleTitle:"Quantitative%20High-Throughput%20Screen%20Identifies%20Inhibitors%20of%20the%20Schistosoma%20mansoni%20Redox%20Cascade",</div><div class="line"> ImagePosition:"3",</div><div class="line"> Citation:"PLoS Negl Trop Dis. 2008 January;2(1):e127.",</div><div class="line"> ncbi_uid:"18235848",</div><div class="line"> link_uid:"PMC2217675"</div><div class="line"> };</div><div class="line"> <span class="tag"></<span class="name">script</span>></span><span class="tag"><<span class="name">script</span> <span class="attr">type</span>=<span class="string">"text/javascript"</span>></span><span class="undefined"></span></div><div class="line"> imageStripObj.images[3]={</div><div class="line"> ImageUrl:"/pmc/articles/instance/2217675/bin/pntd.0000127.g004.jpg",</div><div class="line"> ImageSource:"/pmc/articles/PMC2217675/figure/pntd-0000127-g004/",</div><div class="line"> ThumbUrl:"/pmc/articles/instance/2217675/bin/pntd.0000127.g004.gif",</div><div class="line"> Label:"Figure%204",</div><div class="line"> SourceId:"/pmc/articles/PMC2217675/",</div><div class="line"> CaptionTitle:"Structure%20and%20potency%20(IC50%20in%20%C2%B5M)%20of%20actives%20and%20series%20expansion%20analogues.",</div><div class="line"> Caption:"‘qHTS’ lists the IC50 values obtained from the initial high throughput screen of the collection; ‘confirmation’ represents the IC50 values obtained using the identical assay as in the qHTS from the compounds identified in qHTS and expansion series; ‘TGR Assay’ is the IC50 values obtained in an assay of TGR activity using DTNB as a substrate. NS, not screened (compound not in the screening collection), ND, not determined, NA, not applicable. IC50 values greater than 50 or 57 µM signify lack of fitted curve through the dose-response data, i.e. flat response within the range tested.",</div><div class="line"> ArticleTitle:"Quantitative%20High-Throughput%20Screen%20Identifies%20Inhibitors%20of%20the%20Schistosoma%20mansoni%20Redox%20Cascade",</div><div class="line"> ImagePosition:"4",</div><div class="line"> Citation:"PLoS Negl Trop Dis. 2008 January;2(1):e127.",</div><div class="line"> ncbi_uid:"18235848",</div><div class="line"> link_uid:"PMC2217675"</div><div class="line"> };</div><div class="line"> <span class="tag"></<span class="name">script</span>></span><span class="tag"><<span class="name">script</span> <span class="attr">type</span>=<span class="string">"text/javascript"</span>></span><span class="undefined"></span></div><div class="line"> imageStripObj.images[4]={</div><div class="line"> ImageUrl:"/pmc/articles/instance/2217675/bin/pntd.0000127.g005.jpg",</div><div class="line"> ImageSource:"/pmc/articles/PMC2217675/figure/pntd-0000127-g005/",</div><div class="line"> ThumbUrl:"/pmc/articles/instance/2217675/bin/pntd.0000127.g005.gif",</div><div class="line"> Label:"Figure%205",</div><div class="line"> SourceId:"/pmc/articles/PMC2217675/",</div><div class="line"> CaptionTitle:"Example%20time-course%20plots%20derived%20from%20the%20primary%20screen%2C%20followed%20to%20the%20right%20by%20the%20corresponding%20concentration-response%20curves.",</div><div class="line"> Caption:"(A, B) Non-fluorescent inhibitors, compounds 3 and 14; the decrease in fluorescence is inhibited at increasing compound concentrations while the starting fluorescence remains constant. (C) An example of an apparent activator (Ofloxacin): a highly fluorescent compound which appears to be reacting with one or more components of the assay. Four concentrations out of seven or fifteen are plotted in each of the time course plots for clarity; ▪, 3.2 nM; ▴, 16 nM; □, 10 µM; ▵, 50 µM.",</div><div class="line"> ArticleTitle:"Quantitative%20High-Throughput%20Screen%20Identifies%20Inhibitors%20of%20the%20Schistosoma%20mansoni%20Redox%20Cascade",</div><div class="line"> ImagePosition:"5",</div><div class="line"> Citation:"PLoS Negl Trop Dis. 2008 January;2(1):e127.",</div><div class="line"> ncbi_uid:"18235848",</div><div class="line"> link_uid:"PMC2217675"</div><div class="line"> };</div><div class="line"> <span class="tag"></<span class="name">script</span>></span><span class="tag"></<span class="name">div</span>></span><span class="tag"><<span class="name">script</span> <span class="attr">type</span>=<span class="string">"text/javascript"</span>></span><span class="undefined"></span></div><div class="line"> imageStripObj.containerSelector=".pmc_images";</div><div class="line"> imageStripObj.minWidth=410;</div><div class="line"> 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<ul>
<li><code>urllib.request</code>模块提供一些连接<code>URL</code>并检索其内容的工具</li>
<li>手工查看分隔标签</li>
<li>标记之间最大字符数要结合相关领域文献长度进行适当调整</li>
</ul>
<p>实现代码如下：<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> urllib.request</div><div class="line"><span class="keyword">import</span> re</div><div class="line"></div><div class="line">pmid = <span class="string">'18235848'</span></div><div class="line">url = <span class="string">'http://www.ncbi.nlm.nih.gov/pubmed?term=%s'</span> % pmid</div><div class="line">handler = urllib.request.urlopen(url)</div><div class="line">html = str(handler.read())</div><div class="line"></div><div class="line">title_regexp = re.compile(<span class="string">'<h1>.{5,400}</h1>'</span>)</div><div class="line">title_text = title_regexp.search(html)</div><div class="line">abstract_regexp = re.compile(<span class="string">'<div class=""><p><AbstractText>.{20,3000}</AbstractText></p></div>'</span>)</div><div class="line">abstract_text = abstract_regexp.search(html)</div><div class="line"></div><div class="line">print(<span class="string">'TITLE:'</span>, title_text.group())</div><div class="line">print(<span class="string">'ABSTRACT:'</span>, abstract_text.group())</div></pre></td></tr></table></figure></p>
<p>输出结果如下：<br><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div></pre></td><td class="code"><pre><div class="line">TITLE: <h1>Quantitative high-throughput screen identifies inhibitors of the Schistosoma mansoni redox cascade.</h1></div><div class="line">ABSTRACT: <div class=""><p><AbstractText>Schistosomiasis is a tropical disease associated with high morbidity and mortality, currently affecting over 200 million people worldwide. Praziquantel is the only drug used to treat the disease, and with its increased use the probability of developing drug resistance has grown significantly. The Schistosoma parasites can survive for up to decades in the human host due in part to a unique set of antioxidant enzymes that continuously degrade the reactive oxygen species produced by the host\'s innate immune response. Two principal components of this defense system have been recently identified in S. mansoni as thioredoxin/glutathione reductase (TGR) and peroxiredoxin (Prx) and as such these enzymes present attractive new targets for anti-schistosomiasis drug development. Inhibition of TGR/Prx activity was screened in a dual-enzyme format with reducing equivalents being transferred from NADPH to glutathione via a TGR-catalyzed reaction and then to hydrogen peroxide via a Prx-catalyzed step. A fully automated quantitative high-throughput (qHTS) experiment was performed against a collection of 71,028 compounds tested as 7- to 15-point concentration series at 5 microL reaction volume in 1536-well plate format. In order to generate a robust data set and to minimize the effect of compound autofluorescence, apparent reaction rates derived from a kinetic read were utilized instead of end-point measurements. Actives identified from the screen, along with previously untested analogues, were subjected to confirmatory experiments using the screening assay and subsequently against the individual targets in secondary assays. Several novel active series were identified which inhibited TGR at a range of potencies, with IC(50)s ranging from micromolar to the assay response limit ( approximately 25 nM). This is, to our knowledge, the first report of a large-scale HTS to identify lead compounds for a helminthic disease, and provides a paradigm that can be used to jump-start development of novel therapeutics for other neglected tropical diseases.</AbstractText></p></div></div></pre></td></tr></table></figure></p>
<p>若提取一系列PMID，则可以将PMID放在列表，通过for循环遍历列表<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> urllib.request</div><div class="line"><span class="keyword">import</span> re</div><div class="line"></div><div class="line">pmids = [<span class="string">'18235848'</span>,<span class="string">'22607149'</span>,<span class="string">'21630672'</span>]</div><div class="line"><span class="keyword">for</span> pmid <span class="keyword">in</span> pmids:</div><div class="line"> url = <span class="string">'http://www.ncbi.nlm.nih.gov/pubmed?term=%s'</span> % pmid</div><div class="line"> handler = urllib.request.urlopen(url)</div><div class="line"> html = str(handler.read())</div><div class="line"></div><div class="line"> title_regexp = re.compile(<span class="string">'<h1>.{5,400}</h1>'</span>)</div><div class="line"> title_text = title_regexp.search(html)</div><div class="line"> abstract_regexp = re.compile(<span class="string">'<div class=""><p><AbstractText>.{20,3000}</AbstractText></p></div>'</span>)</div><div class="line"> abstract_text = abstract_regexp.search(html)</div><div class="line"></div><div class="line"> print(<span class="string">'TITLE:'</span>, title_text.group())</div><div class="line"> print(<span class="string">'ABSTRACT:'</span>, abstract_text.group())</div></pre></td></tr></table></figure></p>
<h3 id="检测摘要中特定的词或词组"><a href="#检测摘要中特定的词或词组" class="headerlink" title="检测摘要中特定的词或词组"></a>检测摘要中特定的词或词组</h3><p>实现代码如下：<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div><div class="line">7</div><div class="line">8</div><div class="line">9</div><div class="line">10</div><div class="line">11</div><div class="line">12</div><div class="line">13</div><div class="line">14</div><div class="line">15</div><div class="line">16</div><div class="line">17</div><div class="line">18</div><div class="line">19</div><div class="line">20</div><div class="line">21</div></pre></td><td class="code"><pre><div class="line"><span class="keyword">import</span> urllib.request</div><div class="line"><span class="keyword">import</span> re</div><div class="line"><span class="comment">#word to be searched</span></div><div class="line">keyword = re.compile(<span class="string">'schistosoma'</span>,re.IGNORECASE)</div><div class="line">pmids = [<span class="string">'18235848'</span>,<span class="string">'22607149'</span>,<span class="string">'21630672'</span>]</div><div class="line"><span class="keyword">for</span> pmid <span class="keyword">in</span> pmids:</div><div class="line"> url = <span class="string">'http://www.ncbi.nlm.nih.gov/pubmed?term=%s'</span> % pmid</div><div class="line"> handler = urllib.request.urlopen(url)</div><div class="line"> html = str(handler.read())</div><div class="line"></div><div class="line"> title_regexp = re.compile(<span class="string">'<h1>.{5,400}</h1>'</span>)</div><div class="line"> title_text = title_regexp.search(html)</div><div class="line"> abstract_regexp = re.compile(<span class="string">'<div class=""><p><AbstractText>.{20,3000}</AbstractText></p></div>'</span>)</div><div class="line"> abstract_text = abstract_regexp.search(html)</div><div class="line"> title = title_text.group()</div><div class="line"> abstract = abstract_text.group()</div><div class="line"> word = keyword.search(abstract)</div><div class="line"> <span class="keyword">if</span> word:</div><div class="line"> <span class="comment"># display the title and where the word was found</span></div><div class="line"> print(title)</div><div class="line"> print(word.group(),word.start(),word.end())</div></pre></td></tr></table></figure></p>
<p>输出结果如下：<br><figure class="highlight plain"><table><tr><td class="gutter"><pre><div class="line">1</div><div class="line">2</div><div class="line">3</div><div class="line">4</div><div class="line">5</div><div class="line">6</div></pre></td><td class="code"><pre><div class="line"><h1>Quantitative high-throughput screen identifies inhibitors of the Schistosoma mansoni redox cascade.</h1></div><div class="line">Schistosoma 329 340</div><div class="line"><h1>The redox biology of schistosome parasites and applications for drug development.</h1></div><div class="line">Schistosoma 57 68</div><div class="line"><h1>Investigations of the catalytic mechanism of thioredoxin glutathione reductase from Schistosoma mansoni.</h1></div><div class="line">Schistosoma 70 81</div></pre></td></tr></table></figure></p>
<p>注意在编译时，忽略大小写<br><figure class="highlight python"><table><tr><td class="gutter"><pre><div class="line">1</div></pre></td><td class="code"><pre><div class="line">keyword = re.compile(<span class="string">'schistosoma'</span>,re.IGNORECASE)</div></pre></td></tr></table></figure></p>
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<p>上一期，我们介绍了数据排序相关的内容，这一期按照惯例，我们做几组题目，巩固之前学习的内容<br>
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