Matthew Frosch <frosch at dsg.harvard.edu> wrote:
>> Does anyone know of programs (GCG or otherwise) which are useful in
> determining potential membrane spanning regions based on primary
> sequence data?
> I have a cloned protein which is probably a membrane protein based on
> sequence homology with other proteins. I would like to define the
> membrane spanning domain based on the sequence I have (not just by
> homology with other members of the class).
> Thanks in advance for any guidance.
>> Matthew Frosch
Try the "tmap" program written by Bengt Persson & Patrick Argos.
Here's a part of the readme file.
This program predicts transmembrane segments in proteins,
utilising the algorithm described in:
"Persson, B. & Argos, P. (1994) Prediction of transmembrane
segments in proteins utilsing multiple sequence alignments
J. Mol. Biol. 237, 182-192"
You can find it at ftp.embl-heidelberg.de and the file is
The Scripps Research Institute
yagi2 at scripps.edu