pairwise sequence alignment

[marykindall]

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

[westerman]

bowtie or bowtie2, although overkill for a single reference, will report all alignments. For a short query sequence bowtie is probably better.