Protein variability software

Catherine Letondal letondal at nefertiti.pasteur.fr
Mon Sep 18 06:09:47 EST 2000


In article <39C119F0.4C3F8204 at t10.lanl.gov>, Brian Foley <btf at t10.lanl.gov> writes:
>> 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 ???

What about SC_rate?
http://www.mrc-lmb.cam.ac.uk:80/genomes/jong/SC_rate.html

"A reliability index derived from sequence and composition identity (defined as SC rate) was evaluated against the
accuracy of each alignment position in a database of sequence alignments compared with corresponding structural alignments.
This showed that there is a correlation between SC rate and the alignment error rate for each alignment position,
indicating that it can be used to predict the alignment's reliability systematically. "

-- 
Catherine Letondal -- Pasteur Institute Computing Center







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