EMBOSS: tmap

| ## EMBOSS: tmap

# Program tmap

## Function

Displays membrane spanning regions

## Description

This program predicts transmembrane segments in proteins, utilising the algorithm described in: "Persson, B. & Argos, P. (1994) Prediction of transmembrane segments in proteins utilising multiple sequence alignments J. Mol. Biol. 237, 182-192."

tmap reads in one or more aligned protein sequences.

Two sets of propensity values are then used for the calculations: one for the middle, hydrophobic portion and one for the terminal regions of the transmembrane sequence spans. Average propensity values are calculated for each position along the alignment, with the contribution from each sequence weighted according to its dissimilarity relative to the other alignged sequences.

Eight-residue segments are considered as potential cores of transmembrane segments and elongated if thier middle propensity values are above a threshold. End propensity values are also considered as stop signals. Only helices with a length of 15 to 29 residues are allowed and correctionbs for strictly conserved charged residues are made.

The method is more successful than predictions based upon single sequences alone.

The results are plotted on a graph and written to a text file.

## Usage

Here is a sample session with tmap.

      % tmap sw:opsd_human -out tmap.res

click here for result

## Command line arguments

       Mandatory qualifiers:
      [-msf]               seqset     File containing a sequence alignment
       -graph              xygraph    Graph type

       Optional qualifiers:
       -outfile            outfile    Output file name

       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-msf] (Parameter 1) | File containing a sequence alignment | Readable sequences | Required
-graph | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11
Optional qualifiers | Allowed values | Default
-outfile | Output file name | Output file | tmap.res
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Any protein sequence USA for one or more aligned sequences.

## Output file format

A plot of the propensities to form the middle and the end of transmembrane regions is output.

Bars are displayed in the plot above the regions predicted as being most likely to form transmembrane regions.

The text file (specified by the -output option) gives a summary of these regions. The text file produced by the above example is:

    Program TMAP, version 46, to predict transmembrane segments from .msf file.
    The program reads a multiple alignment file of the GCG multiple sequence format
    and predicts membrane-spanning regions according to the algorithm in
    Persson & Argos (1994), J. Mol. Biol. 237, 182-192.

    RESULTS from program TMAP, edition 46'

    Numbers give: a) number of transmembrane segment
                  b) start of TM segment (alignment position / residue number)
                  c) end of TM segment (alignment position / residue number)
                  d) length of TM segment within parentheses

    PREDICTED TRANSMEMBRANE SEGMENTS FOR ALIGNMENT

      TM  1:   43 -   69  (27.0)
      TM  2:   73 -   97  (25.0)
      TM  3:  112 -  140  (29.0)
      TM  4:  148 -  176  (29.0)
      TM  5:  201 -  229  (29.0)
      TM  6:  255 -  275  (21.0)
      TM  7:  282 -  302  (21.0)

    PREDICTED TRANSMEMBRANE SEGMENTS FOR PROTEIN OPSD_HUMAN

      TM  1:   43 -   69 (27)
      TM  2:   73 -   97 (25)
      TM  3:  112 -  140 (29)
      TM  4:  148 -  176 (29)
      TM  5:  201 -  229 (29)
      TM  6:  255 -  275 (21)
      TM  7:  282 -  302 (21)

The transmembrane regions for the complete alignment are given first, followed by the predictions for each individual sequence in the alignment. (In the example above there is only 1 sequence in the alignment.)

## Data files

None.

## Notes

None.

## References

"Persson, B. & Argos, P. (1994) Prediction of transmembrane segments in proteins utilsing multiple sequence alignments J. Mol. Biol. 237, 182-192."

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

0 if successful.

## Known bugs

None.

## See also

Program name | Description
--- | ---
garnier | Predicts protein secondary structure
helixturnhelix | Report nucleic acid binding motifs
hmoment | Hydrophobic moment calculation
pepcoil | Predicts coiled coil regions
pepnet | Displays proteins as a helical net
pepwheel | Shows protein sequences as helices

## Author(s)

Original program by Bengt Persson and Patrick Argos.

This application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

Completed 17th June 1999.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments