[Bioperl-l] how to not count gaps in the multiple sequence alignment

wenbin mei wenbinmei at gmail.com
Wed Nov 2 00:25:32 EDT 2011


I need some help in coding. I have a multiple sequence alignment which has
gaps. And also I have a reference genome sequence in the alignment which I
know all the coordinates for the protein coding genes. I want to extract
all these protein coding genes alignment from the big alignment. I am using
Bio SimpleAlign but the question is that due to the gaps in the alignment,
the coordinates has shifted in the alignment. I wonder is there a way I can
not count the gaps and still be able to extract the protein alignment. One
way I can do is remove the gaps in the reference first and then extract the
sequence. But I don't like this way ... Thank you for help.


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