[Bioperl-l] genbank (blast) alignments
Robert Buels
rmb32 at cornell.edu
Thu Jul 23 19:38:30 UTC 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
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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