
                                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
