[Bioperl-l] Dumping a MSA from BLAST results

Jason Stajich jason at bioperl.org
Tue Feb 19 16:17:32 UTC 2008

All the individual pairwise alignments won't necessarily be an  
alignment of the same region and the gap insertions can be different  
in each instance of the query sequence that is participating in the  
pairwise alns so it won't fit into an MSA.

It makes more sense to extract the aligned part of the hit sequences  
identified and a subsequence of the query which is the min and max  
region aligned.  Run this through a MSA program.

On Feb 19, 2008, at 6:42 AM, Johan Nilsson wrote:

> Hello,
> I have a question regarding the conversion from a Blast search  
> result (PSI-blast using blastpgp, to be more exact) to a multiple  
> sequence alignment file. I'm running the  
> Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the  
> resulting Bio::Search::Hit::HitI objects. I have no problems  
> obtaining each HSP alignment using $hit->get_aln. However, rather  
> than dumping many local alignments, I would like to write a single  
> result file where the HSPs are interleaved.
> I guess this shouldn't be too hard, but nevertheless I haven't  
> found out how to do this in a simple way. Any suggestions would be  
> highly appreciated!
> Best Regards
> /Johan Nilsson
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