Carnë Draug | 8 Feb 07:57 2013
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getting a Bio::Search::HSP::HSPI from Bio::SimpleAlign (to find differences between sequences)

Hi

I already have a Bio::SimpleAlign object (got it after using TCoffee
through bioperl-run module) and I'm trying to get a
Bio::Search::HSP::HSPI object from a pair of the aligned sequences.
How can I do this? I want to use the seq_inds method to compare the
sequences.

Here's my actual problem just in case I should be trying to fix it
some other way. I have a bunch of sequences from protein isoforms.
They have small differences between them, point-mutations, small
insertions or deletions, nothing too big. I want to make a table of
the mutations that each of them has against the consensus sequence. I
already made the alignment and got have the consensus with
"$align->consensus_string". Now, I want to get something like:

isoform1: Ala67Gly, His90_Met91insGln
isoform2: ....

The seq_inds method from the Bio::Search::HSP::HSPI class seems to do
the part of finding the differences, but how can I get one? I can't
find it on the documentation.

Any tips, and even showing a different approach to my problem, are
most appreciated. Thanks,

Carnë

Gmane