[Bioperl-l] Aligning two alignments ...

Albert Vilella avilella at gmail.com
Wed Mar 28 05:44:03 EDT 2007


You can call the Muscle wrapper with the profile option although when I
wrote it I was assuming 1 aln and a set of seqs as the input:

$alnfilename = /t/data/cysprot.msa';
$seqsfilename = 't/data/cysprot.fa';
$aln = $factory->profile($alnfilename,$seqsfilename);

one could easily add the code for having 2 alns as input, but I think it is
internally the same for muscle,

Cheers,

    Albert.

On 3/27/07, Joshua Udall <jaudall at byu.edu> wrote:
>
> Stephane -
>
> Muscle will align two alignments when you use the
> profile option.  I'm not sure if the 'profile'
> functionality is in the bioperl wrapper or not ...
>
> At 08:12 AM 3/27/2007, Stéphane Téletchéa wrote:
> >Dear all,
> >
> >I'm trying to compare alignments results for small protein sequences to
> >validate my result from another method. In the best option, i would do
> >on two sequences
> >
> >- run a clustalw alignment
> >- run a blast alignment
> >- run a T-Coffee alignment
> >- use my own
> >
> >And align them all to see easily what is identical, what differs.
> >
> >I've considered doing a simple match, but with more than two methods to
> >compare, this may not be trivial. I'd like you opinion on this please.
> >
> >I would consider sequence I as a reference and sequence II as the
> >alignment target.
> >
> >Thanks a lot in advance for your comments,
> >
> >Stéphane
> >--
> >Stéphane Téletchéa, PhD.                  http://www.steletch.org
> >Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
> >INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
> >78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901
> >_______________________________________________
> >Bioperl-l mailing list
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>
> Joshua Udall
> Assistant Professor
> 295 WIDB
> Department of Plant and Animal Science
> Brigham Young University
> Provo, UT 84602
> Office: 801-422-9307
> Fax: 801-422-0008
>
>
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