[Chimera-users] Question about adding a sequence to a previous structural alignment...

Sergio Garay sergio.alberto.garay at gmail.com
Wed Mar 18 05:32:40 PDT 2009

Hi all

I've prepared an structural alignment of my 3 protein templates using
MatchMaker/Match-Align tools.
The question is: when I add my target sequence to the profile obtained in
the step before, Does this
procedure change my previous structural alignment?, or It just aligns the
added sequence to my profile.
The parameters that I used to add my target sequence are: Blosum-62, gap
open, and gap extension
penalties: 12 and 1 respectively.

The second problem I have, its not related to chimera, but may be one of you
can answer it. My target
only has 29 % of identical residues with my templates, so Should I use a
less stringent parameters to
make my alignment?

Any help would be appreciated.

Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221
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