[Bioperl-l] Dumping a MSA from BLAST results

Johan Nilsson johan.nilsson at sh.se
Tue Feb 19 09:42:52 EST 2008


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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