[Bioperl-l] aligning sequences with Bio::Tools::pSW

[Jason Stajich]

You can specify different output formats from the default EMBOSS alignment
report - specifically at least {msf, fasta}.

Local alignments are problematic because you cannot reconstruct where the
alignments came from in the whole seq because of the EMBOSS MSF and
FASTA output formats doesn't necessarily report start/end in the original
seq.

The EMBOSS alignment output format can be parsed with AlignIO::emboss can
parse this format although I still think there are some special cases
where it might not be parsing correctly for local alignments.

-jason
On Fri, 29 Aug 2003, Brian Osborne wrote:

> Bill,
>
> AlignIO does stretcher too? Cool. So that means water, needle, and stretcher
> have the same output format. Are there any others in the EMBOSS suite with
> this output format?
>
> Thanks again,
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of
> william.j.burtle at gsk.com
> Sent: Friday, August 29, 2003 7:56 AM
> To: Joshua Bronson
> Cc: Bioperl list
> Subject: Re: [Bioperl-l] aligning sequences with Bio::Tools::pSW
>
> Joshua,
>
> you might also try the EMBOSS tools (particularly stretcher and needle):
> http://www.emboss.org/
>
> and the bioperl interface:
> http://doc.bioperl.org/releases/bioperl-1.2/Bio/Factory/EMBOSS.html
>
> - Bill Burtle
>
>
>
>
>
>
>
> "Aaron J Mackey" <ajm6q at virginia.edu>
>
> Sent by: bioperl-l-bounces at portal.open-bio.org
> 29-Aug-2003 07:41
> Please respond to "Aaron J. Mackey" <amackey at virginia.edu>
>
>
>
>
>         To:     "Joshua Bronson" <jbronson at acsu.buffalo.edu>
>
>         cc:     "Bioperl list" <bioperl-l at bioperl.org>
>         Subject:        Re: [Bioperl-l] aligning sequences with
> Bio::Tools::pSW
>
>
> pSW.pm is an implementation of the Smith-Waterman algorithm, a *local*
> pairwise alignment algorithm, which means that the best alignment found
> need not start and finish at the beginning and ending of either sequence.
> You seem to want a *global* alignment algorithm, such as Needleman-Wunsch
> (with "free" end-gap penalties for globally aligning the larger sequence:
> this is how to achieve hybrid local/global pairwise alignments); ClustalW
> should be able to give you what you need.
>
> -Aaron
>
> On Thu, 28 Aug 2003, Joshua Bronson wrote:
>
> > I'm interested in the a portion of some virus polyproteins. To find
> > the portion, I'm aligning the polyprotein against other known
> > proteins. I want the computer to give me a best guess and align the
> > smaller protein end-to-end, but currently it's not doing that. It will
> > only give me portions of the protein that align strongly. None of the
> > proteins are aligning end-to-end, unless I align a protein against
> > itself.
> >
> > Bio::Tools:pSW is what I'm using currently. Bioperl doesn't seem to
> > have an interface to do pairwise alignments with Clustalw, and I'm
> > experiencing problems using standalone blast. Anyone have any ideas?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>
> --
>  Aaron J Mackey
>  Pearson Laboratory
>  University of Virginia
>  (434) 924-2821
>  amackey at virginia.edu
>
>
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>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu