Version

Version 2.0c is available in Hippu, Vuori and Murska. The program is for academic use only.

Description

TMHMM is a program for prediction transmembrane helices based on a hidden Markov model. Program reads a fasta fromatted protein sequence and predicts locations of transmembrane, intracellular and extracellular regions.

Usage

You can use TMHMM in Hippu, Vuori and Muska as a command line version. To run the program, give commands:

  module load tmhmm
  tmhmm protein_seq.fasta

A web interface for TMHMM is available in CBS:

http://www.cbs.dtu.dk/services/TMHMM-2.0

Manuals

• A short user manual of TMHMM.

References

A. Krogh, B. Larsson, G. von Heijne, and E. L. L. Sonnhammer.
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes.
Journal of Molecular Biology, 305(3):567-580, January 2001.
(PDF, 959503 bytes)

E. L.L. Sonnhammer, G. von Heijne, and A. Krogh.
A hidden Markov model for predicting transmembrane helices in protein sequences.
In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 175-182, Menlo Park, CA, 1998. AAAI Press.
(Gzipped PostScript, 8 pages, 42470 bytes) (PDF, 844205 bytes)