Pmembr

Pmembr is an improved method to search for related membrane proteins. Here you can paste the sequence of a membrane protein and use this to search against SWISS-PROT (v39) using a combination of membrane region predictions (using TMHMM) and a PSI-BLAST search. It should be noted that this method uses a heuristic search method that is significantly faster than the one used in the Pmembr paper. However the results should be almost identical.

Please paste the Sequence as plain text.

Please give the name of the submission:

and your email adress:

The results will be sent to you by email in a few minutes. Therefore, it is important that your email adress is correct.

or all values

The Pmembr program is freely available under a modified GPL license from here. To use it you also need tmHMM or another membrane prediction program for instance prodiv-TMHMM. You will also need this file to convert the output of tmHMM to our database format

To run pmembr you need to (a) compile the program (b) run tmHMM for your sequence and your databas (c) convert your database to our internal format with plptofast.pl. (d) run psiblast (with these parameters
blastpgp -j 5 -h 1e-5 -m 1 -e 99 -v 10000 -F F
against swissprot) and (e) run it with this command.
pmembr2 -prof FILE.plp FILE.psi - DATABASE
If you want to run faster you can use our heuristic search method (pmembrh) instead of pmembr2.

You can download the GPCR and sequences used for testing. And also the complete database including TM predictions from TMHMM. The results from all predictions are available in this file. Please read the README file for descriptions. The specsens vailes are in the spec_sens.dat files.

To get TMHMM you need to contact Anders Krogh or use our novel HMM program modHMM.