[Bioperl-l] genbank (blast) alignments

Robert Buels rmb32 at cornell.edu
Thu Jul 23 15:38:30 EDT 2009

Wow, that silence is deafening.  I can't believe somebody who knows what 
they're talking about hasn't written you back yet.

Perhaps you could do some kind of transformation where you read in the 
BLAST report with Bio::SearchIO, and then write to MSF with 
Bio::AlignIO::msf?  You would probably need to do some fiddling to 
create the proper objects and relationships that Bio::AlignIO::msf would 

But this reply probably isn't helpful, because you probably already knew 
that much.  I'm mostly just trying to add to this thread so that people 
who actually know a lot about BioPerl's functions in this area will see 
it and hopefully be of more help.


Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu

Thomas Keller wrote:
> Greetings,
> Blast 2.2.21 has a multi-sequence alignment feature that is really 
> handy: put in the accession number of the refseq in one sequence field 
> and a concatenated fasta file of the Sanger reads to align in the second 
> box and it does the alignments. Unfortunately, the output is a series of 
> alignments rather than the more useful msf format with all reads aligned 
> with the reference.
> Is there a bioperl module that reads the blast alignments and converts 
> it to an msf alignment?
> thanks,
> Tom
> kellert at ohsu.edu
> 503-494-2442
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