July 2001: TMHMM has been rated best in an independent comparison of programs for prediction of TM helices:
TMHMM is described in
Please cite.
Press here to see other material (training data, etc).
This is an example (one protein):
>5H2A_CRIGR you can have comments after the ID
MEILCEDNTSLSSIPNSLMQVDGDSGLYRNDFNSRDANSSDASNWTIDGENRTNLSFEGYLPPTCLSILHL
QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYRWP
LPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGVSMPIPVF
GLQDDSKVFKQGSCLLADDNFVLIGSFVAFFIPLTIMVITYFLTIKSLQKEATLCVSDLSTRAKLASFSFL
PQSSLSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNE
HVIGALLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENRKPLQLILVNTIPALAYKSSQLQA
GQNKDSKEDAEPTDNDCSMVTLGKQQSEETCTDNINTVNEKVSCV
cat seq.fasta | tmhmmor
tmhmm seq.fastaBoth versions can take several files with several proteins in each. You can edit the tmhmm script (perl5) to your liking.
You can also by-pass the script and run the program directly
where <path> is the directory of the TMHMM files.cat seq.fasta | decodeanhmm -f <path>/TMHMM2.0.options -modelfile <path>/TMHMM2.0.model
decodeanhmm takes some options that
are specified in TMHMM2.0.options.
Take a look at that file if you don't like the output. These options
can also be given on the command line.
Here is an example:
# 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
If the whole sequence is labeled as inside or outside, the prediction
is that it contains no membrane
helices. It is probably not wise to interpret it as a prediction
of location. The prediction gives the most probable location and orientation
of transmembrane helices in the sequence. It is found by an algorithm called
N-best (or 1-best in this case) that sums over all paths through the model
with the same location and direction of the helices.
The first few lines gives some statistics:
Length: the length of the protein sequence. Number of predicted TMHs: The number of predicted transmembrane helices. Exp number of AAs in TMHs: The expected number of amino acids intransmembrane helices. If this number is larger than 18 it is very likely to be a transmembrane protein (OR have a signal peptide). Exp number, first 60 AAs: The expected number of amino acids in transmembrane helices in the first 60 amino acids of the protein. If this number more than a few, you should be warned that a predicted transmembrane helix in the N-term could be a signal peptide. Total prob of N-in: The total probability that the N-term is on the cytoplasmic side of the membrane. POSSIBLE N-term signal sequence: a warning that is produced when "Exp number, first 60 AAs" is larger than 10.
At the top of the plot (between 1 and 1.2) the N-best prediction is shown.
The plot is obtained by calculating the total probability that a residue sits in helix, inside, or outside summed over all possible paths through the model. Sometimes it seems like the plot and the prediction are contradictory, but that is because the plot shows probabilities for each residue, whereas the prediction is the over-all most probable structure. Therefore the plot should be seen as a complementary source of information.
Below the plot there are links to
For the example above the short output would be (except that it would be on one line):"len=": the length of the protein sequence. "ExpAA=": The expected number of amino acids intransmembrane helices (see above). "First60=": The expected number of amino acids in transmembrane helices in the first 60 amino acids of the protein (see above). "PredHel=": The number of predicted transmembrane helices by N-best. "Topology=": The topology predicted by N-best.
COX2_BACSU
len=278
ExpAA=68.69
First60=39.89
PredHel=3
Topology=i7-29o44-66i87-109o
The topology is given as the position of the transmembrane helices separated
by 'i' if the loop is on the inside or 'o' if it is on the outside. The
above example 'i7-29o44-66i87-109o' means that it starts on the inside,
has a predicted TMH at position 7 to 29, the outside, then a TMH at position
44-66 etc.
One of the most common mistakes by the program is to reverse the direction of proteins with one TM segment.
Do not use the program to predict whether a non-membrane protein is
cytoplasmic or not.