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

[Brian Osborne]

Jason,

I guess I'm asking something simpler, and I'm not an EMBOSS user. Which of
the EMBOSS alignment programs use this "default EMBOSS alignment" format,
aside from water, needle, and stretcher. All of them? Currently the docs
just say water and needle, which isn't exactly right.

Apart from the issue, admittedly important, about loss of the initial or
input coordinates.

Brian O.

-----Original Message-----
From: Jason Stajich [mailto:jason at cgt.duhs.duke.edu]
Sent: Friday, August 29, 2003 1:02 PM
To: Brian Osborne
Cc: william.j.burtle at gsk.com; Joshua Bronson; Bioperl list
Subject: RE: [Bioperl-l] aligning sequences with Bio::Tools::pSW

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