[Bioperl-l] genbank (blast) alignments

[Mark A. Jensen]

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.

cheers, 
MAJ
 
----- 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
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