Rather than searching through each query sequence for possible motifs, instead anchor the motif identification to a given location in each sequence. This is ideal for the special case where you want to look for DNA structure in instances where you know the bp spacing is fixed.
Could be implemented by including an --anchored_offset INT flag which takes an integer value to specify the offset from a set position in each sequence and an --anchored_pos LOC which specifies whether the offset is relative to the center, 5' end, or 3' end of each sequence.
Code would need to be modifying to skip motif searching through all windows in each sequence and instead to only consider the windows defined by the anchored options.
Rather than searching through each query sequence for possible motifs, instead anchor the motif identification to a given location in each sequence. This is ideal for the special case where you want to look for DNA structure in instances where you know the bp spacing is fixed.
Could be implemented by including an
--anchored_offset INTflag which takes an integer value to specify the offset from a set position in each sequence and an--anchored_pos LOCwhich specifies whether the offset is relative to the center, 5' end, or 3' end of each sequence.Code would need to be modifying to skip motif searching through all windows in each sequence and instead to only consider the windows defined by the
anchoredoptions.