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What is TMhmm ?

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

More: http://www.cbs.dtu.dk/services/TMHMM/

References:

Sonnhammer, E., et al. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. ISMB, 6, 175-182.

Krogh, A., et al. (2001) Prediction transmembrane protein topology with a hidden markov model: application to complete genomes. J. Mol. Biol., 305, 567-580

How to read TMhmm results

The table of results indicates the begin and end positions of detected alpha-helices for the protein sequence. It also gives the location (inside/outside) of the fragments in between the helices.

Tips: As protein can be called « membranar » if it contains more than 3 alpha-helices.