[Bioperl-l] genbank (blast) alignments

Mark A. Jensen maj at fortinbras.us
Thu Jul 23 21:20:32 UTC 2009

In my experience on the list, everyone gets helped as soon as it is
possible for the extremely busy people who do the helping make
time for it. For example, I trolled the list in my limited free time the
other night and answered two outstanding questions. Of course, 
I encourage others to do the same, and they do. One thing I tend
not to do is to lay the guilt trip on already busy people. I find this
helps me in later interactions, presently unimagined, with those busy
and influential persons.

The culture may be different for other open source projects. I have
found a good strategy here to be: provide the help with minimal editorial
comment (either on others' response, or your own), and let the help
you provide speak for itself and accumulate over time.

----- Original Message ----- 
From: "Robert Buels" <rmb32 at cornell.edu>
To: "Thomas Keller" <kellert at ohsu.edu>
Cc: "BioPerl-List" <bioperl-l at bioperl.org>
Sent: Thursday, July 23, 2009 3:38 PM
Subject: Re: [Bioperl-l] genbank (blast) alignments

> 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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