Hi all<br><br>I&#39;ve prepared an structural alignment of my 3 protein templates using MatchMaker/Match-Align tools. <br>The question is: when I add my target sequence to the profile obtained in the step before, Does this<br>
procedure change my previous structural alignment?, or It just aligns the added sequence to my profile.<br>The parameters that I used to add my target sequence are: Blosum-62, gap open, and gap extension<br>penalties: 12 and 1 respectively.<br>
<br>The second problem I have, its not related to chimera, but may be one of you can answer it. My target<br>only has 29 % of identical residues with my templates, so Should I use a less stringent parameters to<br>make my alignment?<br>
<br>Any help would be appreciated.<br><br clear="all"><br>-- <br>Dr. Sergio Garay<br>Facultad de Bioquimica y Cs. Biológicas<br>Universidad Nacional del Litoral<br>Santa Fe - Argentina<br>C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA<br>
Argentina<br>Ph. +54 (342) 4575-213<br>Fax. +54 (342) 4575-221 <br>