Aim
Annotate a-helices, b-sheets, and loops of mitochondiral protein cytochrome b
Background
Protein structural motif metadata can help make sense of nucleotide variation. Motifs include alpha-helices, beta-sheets, loops, internal and external exposed amino acids, extracellular, intracellular, and transmembrane domains.
Method
Start by reading this paper.
Data
Use sequence A07 from here:
deepcelllineage/data01/gen/nguyen_nc_2018/20190710-320lfastas/
(data01 is a repo within deepcelllineage)
A link to the files is here:
https://github.com/deepcelllineage/data01/tree/master/gen/nguyen_nc_2018/20190710-320lfastas
These are .fasta files that are the full length of the mitochondrial gene plus some of chr1. There is a separate issue to chop off the chr1 part.
Document your learning process
Please fork & clone this repo. Check out a branch for your work, then push and make a PR for us to merge your note and files.
Add a note (can be .md or .ipynb) with your steps in mitolin/nb.
Your note should be named as follows:
- DATE-issue#-shortdescription.ext
e.g.:
- 20190701-i11-annotate-cb-abloop.md
Questions?
Please put questions related to this issue in this issue thread.
If you want a quick response, post a link to your comment in this thread to Slack #deepcelllineage and tag @deena or others. You can also DM @deena.
To join Slack enter your email address here. For questions NOT specifically related to this issue, get in touch through any of the communication methods listed in DCL's overview README.
Aim
Annotate a-helices, b-sheets, and loops of mitochondiral protein cytochrome b
Background
Protein structural motif metadata can help make sense of nucleotide variation. Motifs include alpha-helices, beta-sheets, loops, internal and external exposed amino acids, extracellular, intracellular, and transmembrane domains.
Method
Start by reading this paper.
Data
Use sequence A07 from here:
deepcelllineage/data01/gen/nguyen_nc_2018/20190710-320lfastas/
(data01 is a repo within deepcelllineage)
A link to the files is here:
https://github.com/deepcelllineage/data01/tree/master/gen/nguyen_nc_2018/20190710-320lfastas
These are .fasta files that are the full length of the mitochondrial gene plus some of chr1. There is a separate issue to chop off the chr1 part.
Document your learning process
Please fork & clone this repo. Check out a branch for your work, then push and make a PR for us to merge your note and files.
Add a note (can be .md or .ipynb) with your steps in mitolin/nb.
Your note should be named as follows:
e.g.:
Questions?
Please put questions related to this issue in this issue thread.
If you want a quick response, post a link to your comment in this thread to Slack #deepcelllineage and tag @deena or others. You can also DM @deena.
To join Slack enter your email address here. For questions NOT specifically related to this issue, get in touch through any of the communication methods listed in DCL's overview README.