[Bioperl-l] Aligning two alignments ...
Derek.Fairley at bll.n-i.nhs.uk
Wed Mar 28 04:04:23 EDT 2007
You might also want to take a look at TuneClustalX
This utility compares the Q-score values generated by ClustalX when run with different gap penalties, to optimize your aa alignment in the first place.
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Stéphane Téletchéa
Sent: 27 March 2007 16:13
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Aligning two alignments ...
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
Thanks a lot in advance for your comments,
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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