TMHMM

From BioPerl

Description

TMHMM -- TransMembrane prediction using Hidden Markov Models -- is a program for predicting transmembrane helices based on a hidden Markov model. It reads a FASTA formatted protein sequence and predicts locations of transmembrane, intracellular and extracellular regions.

Web site

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

Example "long" output

# COX2_BACSU Length: 278
# COX2_BACSU Number of predicted TMHs:  3
# COX2_BACSU Exp number of AAs in TMHs: 68.6888999999999
# COX2_BACSU Exp number, first 60 AAs:  39.8875
# COX2_BACSU Total prob of N-in:        0.99950
# COX2_BACSU POSSIBLE N-term signal sequence
COX2_BACSU        TMHMM2.0        inside       1     6
COX2_BACSU        TMHMM2.0        TMhelix      7    29
COX2_BACSU        TMHMM2.0        outside     30    43
COX2_BACSU        TMHMM2.0        TMhelix     44    66
COX2_BACSU        TMHMM2.0        inside      67    86
COX2_BACSU        TMHMM2.0        TMhelix     87   109
COX2_BACSU        TMHMM2.0        outside    110   278 

References

1. Error fetching PMID 9783223: [tmhmm1998]
2. Error fetching PMID 11152613: [tmhmm2001]
3. Error fetching PMID 12482603: [tmhmm2002]
4. Error fetching PMID 15111065: [tmhmm2004]