[Bioperl-l] Stop him before he codes again![almost-multiple-alignment tool?]

Joseph Bedell jbedell at oriongenomics.com
Mon Jul 25 10:04:26 EDT 2005

Hey George,

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
>-----Original Message-----
>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-
>alignment tool?]
>Yep, there's nothing scarier than some people at the keyboard....
>I have:
>  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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