[Bioperl-l] Aligning two alignments ...

Joshua Udall jaudall at byu.edu
Tue Mar 27 11:36:35 EDT 2007


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
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Joshua Udall
Assistant Professor
295 WIDB
Department of Plant and Animal Science
Brigham Young University
Provo, UT 84602
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