[Biopython] Mapping positions in a pairwise alignment

[Lior Glick]

Hi all,

I have a pairwise alignment of protein sequences, created with Bio.pairwise2,
something like this:

C-GGLK-GAPFLAC||||||||||||||
CHG--KTGASFLQC

I would like to know which position in the subject sequence is aligned to
which position in the query sequence. In this example if the top sequence
is the subject than I would like to know that position 1 in subject is
aligned to position 1 in query, 2 is aligned to 3, 5 to 4, 6 to 6 etc...

Does Biopython have this functionality, or do I have to write my own
function? Any suggestions?

Thanks!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20150616/66c59a09/attachment.html>