Protein variability software

Raf Podowski Raf.Podowski at cgr.ki.se
Mon Sep 18 05:42:45 EST 2000


William COHEN wrote:

>  Hello,Does anyone know a software which can be use to calculate a
> consensus sequence AND the variability in aminoacid at each position
> of the sequence from  100 or 200 protein sequences ???

The belvu program
(http://www.cgr.ki.se/cgr/groups/sonnhammer/Belvu.html) will print a
table with consensus residue at each position and the identity and
conservation fractions.  Use :  belvu -c <alignment>
You can also get a plot of the conservation profile while displaying the
alignment.
Otherwise the HMMER + SAM combination of programs will produce similar
data.


--
Raf M. Podowski
Center for Genomics Research
Karolinska Institutet
17177 Stockholm
Sweden


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