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Transmembrane Protein

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Sat May 13 06:16:36 EST 1995


In <3ovp6q$fkp at cisunix1.dfci.harvard.edu> Matthew writes:

> 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).  

Here are two postings that may help:

---> cut here >--------------------------------------------------------------->
Newsgroups: bionet.software
Subject: Re: finding trans-membrane domains of proteins
Message-ID: <1994Apr22.081426.22115 at netnews.smithkline.com>
From: tennant at hau410 (Mike Tennant)
Date: Fri, 22 Apr 1994 08:14:26 GMT
Organization: SmithKline Beecham Pharmaceuticals

Bengt Persson's prog 'tms-predict' is an information derived package
which he has shown to be able to detect all but 5 of the putative
trans-membrane regions in the swiss-prot database. It is based on
multiple sequence alignments (nominally from pileup in GCG).
Apparently it will be deposited on the EMBL server shortly (ftp to
felix.embl-heidelberg.de)


Newsgroups: bionet.software
Subject: Re: finding trans-membrane domains of proteins
Message-ID: <1994Apr23.101937.51251 at ucl.ac.uk>
From: jones at bsm.biochemistry.ucl.ac.uk (David Jones)
Date: 24 Apr 1994 05:09:10 -0500
Organization: University College London

john f hess phd (jfhess at ucdavis.edu) wrote:
> Howdy everyone, 

> This seems to be the place to ask this question. I am interested in
> programs that will analyze protein sequences and tell me where potential
> trans-membrane domains are. 

> I am currently using MacDNAsis on my mac and have GCG on a vax on main
> campus. If a shareware program is available at indiana or ? please let me
> know. Alternatively, I can check the rest of UCD for some other
> commercially available program that does what I want.

A PC executable version of our transmembrane protein prediction program
MEMSAT is available via anonymous FTP from ftp.biochem.ucl.ac.uk
(128.40.46.11) - download the files in pub/MEMSAT. It's also available
from the EMBL file server. This program implements a new method we have
developed to not only accurately locate tm regions, but to work out the
optimum topology (i.e. whether each tm points into or out of the membrane)
as well (see Biochemistry vol 33 p3048 for details). The C source code is
available via e-mail (see the README file on ftp.biochem), and this should
compile on most platforms - though I haven't a Mac to try it on, VAX should
be OK. If anyone manages to compile it on a Mac I'd be interested to know.

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This message was written, produced and executively directed by Dr David Jones
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---> end cut here >----------------------------------------------------------->

Regards,
   Christoph Gartmann


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