TMHMM 2.0 - DTU Health Tech (2024)


At most 10,000 sequences and 4,000,000 amino acids per submission; each sequence not more than 8,000 amino acids.

The sequences are kept confidential and will be deleted after processing.

TMHMM-2.0 Guide

This server is for prediction of transmembrane helices in proteins.

July 2001:TMHMM has been rated best in an independent comparison of programsfor prediction of TM helices:

  • S.Moller, M.D.R.Croning, R.Apweiler.
    Evaluation of methods for the prediction of membrane spanning regions.
    Bioinformatics, 17(7):646-653, July 2001.(medline)

Quote from the abstract:
`Our results show that TMHMM is currently the best performing transmembraneprediction program.'

TMHMM is described in

  • 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)

Please cite.

Press here to see other material (training data, etc).


The program takes proteins in FASTA format. It recognizesthe 20 amino acids and B, Z, and X, which are all treated equally as unknown.Any other character is changed to X, so please make sure the sequencesare sensible proteins

This is an example (one protein):

>5H2A_CRIGR you can have comments after the ID

How to run it

Either give the name of the local file in which you have the proteins inthe top half of the window, or paste the sequence(s) into the lower partof the window. Then press `Submit'. (It should be possible to bothgive it a local file and paste sequences if you really want.)


There are two output formats: Long and short.

Long output format

For the long format (default), tmhmmgives some statistics and a list of the location of the predicted transmembranehelices and the predicted location of the intervening loop regions.

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 TMHMM2.0inside 1 6
COX2_BACSU TMHMM2.0TMhelix 7 29
COX2_BACSU TMHMM2.0outside 30 43
COX2_BACSU TMHMM2.0TMhelix 44 66
COX2_BACSU TMHMM2.0inside 67 86
COX2_BACSU TMHMM2.0TMhelix 87 109
COX2_BACSU TMHMM2.0outside 110 278

If the whole sequence is labeled as inside or outside, the predictionis that it contains no membrane
helices. It is probably not wise to interpret it as a predictionof location. The prediction gives the most probable location and orientationof transmembrane helices in the sequence. It is found by an algorithm calledN-best (or 1-best in this case) that sums over all paths through the modelwith 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 intransmembranehelices. If this number is larger than 18 it is very likely to be a transmembraneprotein (OR have a signal peptide).
  • Exp number, first 60 AAs: The expected number of amino acids in transmembranehelices in the first 60 amino acids of the protein. If this number morethan a few, you should be warned that a predicted transmembrane helix inthe N-term could be a signal peptide.
  • Total prob of N-in: The total probability that the N-term is on the cytoplasmicside of the membrane.
  • POSSIBLE N-term signal sequence: a warning that is produced when "Exp number,first 60 AAs" is larger than 10.
  • Plot of probabilities

    The plot shows the posterior probabilitiesof inside/outside/TM helix. Here one can see possible weak TM helices thatwere not predicted, and one can get an idea of the certainty of eachsegment in the prediction.

    At the top of the plot (between 1 and 1.2) the N-best prediction isshown.

    The plot is obtained by calculating the total probability that aresidue sits in helix, inside, or outside summed over all possiblepaths through the model. Sometimes it seems like the plot and theprediction are contradictory, but that is because the plot shows probabilitiesfor each residue, whereas the prediction is the over-all most probablestructure. Therefore the plot should be seen as a complementary sourceof information.

    Below the plot there are links to

    • The plot in encapsulated postscript
    • A script for making the plot in gnuplot.
    • The data for the plot.

    Short output format

    In the short output format one line is produced for each protein with nographics. Each line starts with the sequence identifier and then thesefields:

  • "len=": the length of the protein sequence.
  • "ExpAA=": The expected number of amino acids intransmembrane helices (seeabove).
  • "First60=": The expected number of amino acids in transmembranehelices 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.
  • For the example above the short output would be (except that it would beon one line):


    The topology is given as the position of the transmembrane helices separatedby 'i' if the loop is on the inside or 'o' if it is on the outside. Theabove 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 position44-66 etc.

    Final remarks

    Predicted TM segments in the n-terminal region sometime turn out to besignal peptides.

    One of the most common mistakes by the program is to reverse the directionof proteins with one TM segment.

    Do not use the program to predict whether a non-membrane protein iscytoplasmic or not.

    Software Downloads

    • Version 2.0c
      • SunOS
      • OSF1
      • Linux
      • IRIX64
      • IRIX32
      • AIX
    TMHMM 2.0 - DTU Health Tech (2024)
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