[Bioperl-l] Aligning two alignments ...

Fairley, Derek Derek.Fairley at bll.n-i.nhs.uk
Wed Mar 28 04:04:23 EDT 2007


Stéphane,

You might also want to take a look at TuneClustalX
(http://homepage.mac.com/barryghall/TuneClustalX.html).

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.

Derek.


-----Original Message-----
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 ...

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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