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Subject: Re: Bioinformatics Toolbox
Date: Fri, 6 Nov 2009 14:15:06 +0000 (UTC)
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Look at the recently added function "localalign". If you have an old version of the toolbox by changing your sequences to profiles you can use profalign with the terminalgapadjust option set to  false.
HTH
Lucio

"H " <harpreetj@gmail.com> wrote in message <hcvulq$bba$1@fred.mathworks.com>...
> How to compute Fit Alignment using Matlab?  (Semiglobal Alignment)