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 successfull.

Known bugs

None.

See also

Program nameDescription
garnierPredicts protein secondary structure
helixturnhelixReport nucleic acid binding motifs
hmomentHydrophobic moment calculation
pepcoilPredicts coiled coil regions
pepnetDisplays proteins as a helical net
pepwheelShows 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