[Bioperl-l] EMBOSS Alignment program [was aligning sequences with Bio::Tools::pSW]

[Jason Stajich]

Any of the programs which provide the -aformat option I guess.  I don't
think demoalign is really part of the distro though so safe to ignore it.

[jason at sonogno acd]$ pwd
/usr/local/pkg/emboss/share/EMBOSS/acd

[jason at sonogno acd]$ grep "aformat:" *
demoalign.acd:  aformat: "SRS"
matcher.acd:  aformat: "markx0"
merger.acd:  aformat: "simple"
needle.acd:  aformat: "srspair"
stretcher.acd:  aformat: "markx0"
supermatcher.acd:  aformat: "simple"
water.acd:  aformat: "srspair"



On Fri, 29 Aug 2003, Brian Osborne wrote:

> 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
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu