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Old 03-13-2014, 08:59 AM   #1
marykindall
Junior Member
 
Location: newyork

Join Date: Mar 2014
Posts: 1
Default pairwise sequence alignment

This is a primitive question but somehow I could not find a solution to it. I have two sequences 'large' and 'small' as given below.

>large
XXXXXXXXXXXXXXXXXXXGGGTTVTTSSAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBGGGTTLTTSS


>small
GGGTTVTTSS


I need to align the 'small' sequence to the 'large' sequence. Clearly there are two places where it can be aligned. I need to get indices of both the locations. I was trying BioPython's "pairwise2.align.globalms" function but it is only able to align to the second position.



pairwise2.align.globalms(largeStr, smallStr, 2, -1, -1, 0, penalize_end_gaps=False)
Ans:
[('XXXXXXXXXXXXXXXXXXXGGGTTVTTSSAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBGGGTTLTTSS',
'-----------------------------------------------------------------------------------------GGGTTLTTSS',
20.0,
0,
99)]



Which parameter can I change here or which other pachage/lightweight free software can compute this?

Thanks
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Old 03-13-2014, 12:32 PM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
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bowtie or bowtie2, although overkill for a single reference, will report all alignments. For a short query sequence bowtie is probably better.
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