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

[william.j.burtle at gsk.com]

Most of the EMBOSS tools let you specify an "aformat" flag.  See toward 
the bottom of:

http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignFormats.html


Here is a code snippet (using 'matcher').  In this particular case, I had 
specified "pair" format, and 2 alternatives (i.e., the top two hits):


  my $factory = new Bio::Factory::EMBOSS(-verbose => undef);
  my $prog = $factory->program('matcher');

  $prog->run({ '-sequencea' => Bio::Seq->new(-id => "seq1", -seq => 
$seq1),
               '-sequenceb' => Bio::Seq->new(-id => "seq2", -seq => 
$seq2),
               '-aformat'   => "pair",
               '-alternatives' => 2,
               '-outfile'   => $outfile});


## later in the program.....

  my $alignio_fmt = "emboss";
  my $align_res = new Bio::AlignIO(-format => $alignio_fmt,
                                   -file   => $outfile);




- Bill






"Brian Osborne" <brian_osborne at cognia.com>

Sent by: bioperl-l-bounces at portal.open-bio.org
29-Aug-2003 12:25

 
 

        To:     william.j.burtle at gsk.com, "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

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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