[Bioperl-l] genbank (blast) alignments

Jason Stajich jason at bioperl.org
Thu Jul 23 16:00:51 EDT 2009

HSP->get_aln will give you the pairwise alignment as a multiple  
sequence aln object but the short answer is there is not a parser for  
the multi-sequence alignment format from BLAST that I know of -- you  
might want to post the example format so we can more easily figure out  
how different it is from the supported parsers in Bio::AlignIO

On Jul 23, 2009, at 1:38 PM, Robert Buels wrote:

> 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 want.
> 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.
> Rob
> -- 
> 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
> http://www.sgn.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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Jason Stajich
jason at bioperl.org

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