[Bioperl-l] Stop him before he codes
jbedell at oriongenomics.com
Mon Jul 25 10:04:26 EDT 2005
Have you looked at the display option of -m 1 in NCBI BLAST? That gives
a multiple sequence alignment-like output.
Joseph A Bedell, Ph.D. office: 314-615-6979
Director, Bioinformatics fax: 314-615-6975
Orion Genomics cell: 314-518-1343
4041 Forest Park Ave
St. Louis, MO 63108
>From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
>bounces at portal.open-bio.org] On Behalf Of George Hartzell
>Sent: Saturday, July 23, 2005 3:45 PM
>To: BioPerl MailingList
>Subject: [Bioperl-l] Stop him before he codes again![almost-multiple-
>Yep, there's nothing scarier than some people at the keyboard....
> 1 putative sequence (DNA, not too big 1-5kb).
> many (1-10) empirically determined sequences (DNA) that should be
> fairly similar to the putative sequence.
>It's trivial to:
> produce a pairwise alignment of each empirical sequence against the
> putative sequence.
>I'd ultimately like to produce (actually, I don't have much choice...):
> an almost multiple-alignment-like figure, with the putative sequence
> (e.g.) along the bottom and the empirical sequences piled up above
> it, gapped in emp. and put. sequences where necessary.
>It's pretty much similar to piling up a bunch of EST's/cDNA vs. the
>corresponding genomic, with a simpler gapping model (no splicing,
>Ideally I'd like to just wave my hands and have it all work :). I'll
>write code if I have to....
>Since I'm not really looking for a multiple alignment, I'd like to
>avoid the cost of actually computing/approximating one.
>I'd like to just do the pairwise alignments then shoehorn the results
>into an existing bioperl multiple-alignment representation and play
>with it from there.
>I'd love comments (and will happily pay in beer/coffee next time
>you're in Berkeley) about:
> - existing tools that do just this (or even close)
> - what's the cleanest bioperl object to shoehorn it into?
> SimpleAlign? Align?
> - given one of those objects, are where should I start digging for
> pretty output routines?
> - if there's nothing particularly useful, any suggestions on how
> to structure things so that I can deposit them into BioPerl?
> - should i just punt and run something (e.g. clustalw, pileup)
> against the putative and all the empirical and be done with it?
> Tool recommendations?
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