                                    tmap



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Function

   Predict and plot transmembrane segments in protein sequences

Description

   tmap predicts transmembrane segments for an aligned set of protein
   sequences, 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.". 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
   transmembrane regions for the complete alignment are given first,
   followed by the predictions for each individual sequence in the
   alignment.

Usage

   Here is a sample session with tmap


% tmap opsd.msf -out tmap.res -graph cps
Predict and plot transmembrane segments in protein sequences

Created tmap.ps


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Predict and plot transmembrane segments in protein sequences
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     File containing a protein sequence alignment
   -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)
  [-outfile]           report     [*.tmap] Output report file name (default
                                  -rformat seqtable)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequences" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   "-outfile" associated qualifiers
   -rformat2           string     Report format
   -rname2             string     Base file name
   -rextension2        string     File name extension
   -rdirectory2        string     Output directory
   -raccshow2          boolean    Show accession number in the report
   -rdesshow2          boolean    Show description in the report
   -rscoreshow2        boolean    Show the score in the report
   -rstrandshow2       boolean    Show the nucleotide strand in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

   tmap reads a set of aligned protein sequences.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Input files for usage example

  File: opsd.msf

!!AA_MULTIPLE_ALIGNMENT 1.0

  opsd.msf MSF:  354 Type: P 15/07/06 CompCheck: 5414 ..

  Name: OPSD_HUMAN Len: 354  Check: 2647 Weight: 50.00
  Name: OPSD_XENLA Len: 354  Check: 2767 Weight: 50.00

//

           1                                               50
OPSD_HUMAN MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
OPSD_XENLA MNGTEGPNFYVPMSNKTGVVRSPFDYPQYYLAEPWQYSALAAYMFLLILL

           51                                             100
OPSD_HUMAN GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
OPSD_XENLA GLPINFMTLFVTIQHKKLRTPLNYILLNLVFANHFMVLCGFTVTMYTSMH

           101                                            150
OPSD_HUMAN GYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE
OPSD_XENLA GYFIFGPTGCYIEGFFATLGGEVALWSLVVLAVERYIVVCKPMANFRFGE

           151                                            200
OPSD_HUMAN NHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNN
OPSD_XENLA NHAIMGVAFTWIMALSCAAPPLFGWSRYIPEGMQCSCGVDYYTLKPEVNN

           201                                            250
OPSD_HUMAN ESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV
OPSD_XENLA ESFVIYMFIVHFTIPLIVIFFCYGRLLCTVKEAAAQQQESLTTQKAEKEV

           251                                            300
OPSD_HUMAN TRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
OPSD_XENLA TRMVVIMVVFFLICWVPYAYVAFYIFTHQGSNFGPVFMTVPAFFAKSSAI

           301                                            350
OPSD_HUMAN YNPVIYIMMNKQFRNCMLTTICCGKNPLGD.DEASATVSKTETSQVAPA~
OPSD_XENLA YNPVIYIVLNKQFRNCLITTLCCGKNPFGDEDGSSAATSKTEASSVSSSQ

           351
OPSD_HUMAN ~~~~
OPSD_XENLA VSPA


Output file format

   The output is to the specified graphics device.

   The results can be output in one of several formats by using the
   command-line qualifier -graph xxx, where 'xxx' is replaced by the name
   of the required device. Support depends on the availability of
   third-party software packages.

   The device names that output to a file are: ps (postscript), cps
   (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.

   The other available device names are: meta, x11 (xwindows), tek
   (tek4107t), tekt (tektronix), xterm, text.

   Output can be turned off by specifying none (null).

   See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further
   information on supported devices.

   The output is a standard EMBOSS report file.

   The results can be output in one of several styles by using the
   command-line qualifier -rformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq,
   draw, restrict, excel, feattable, motif, nametable, regions, seqtable,
   simple, srs, table, tagseq.

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   By default the output is in 'seqtable' format.

  Output files for usage example

  File: tmap.res

########################################
# Program: tmap
# Rundate: Sun 15 Jul 2012 12:00:00
# Commandline: tmap
#    [-sequences] ../../data/opsd.msf
#    -outfile tmap.res
#    -graph cps
# Report_format: seqtable
# Report_file: tmap.res
########################################

#=======================================
#
# Sequence: Consensus     from: 1   to: 354
# HitCount: 7
#=======================================

  Start     End TransMem Sequence
     43      70        1 YMFLLIvLG-PINFlTLyVTvQHKKLRT
     71      98        2 PLNYILLNL--Ad-FMVL-GFT-TlYTS
    112     140        3 lEGFFATLGGEiALWSLVVLAiERYvVVC
    148     176        4 FGENHAIMGVAFTWvMALaCAAPPL-GWS
    201     229        5 ESFVIYMFvVHFTIPmIiIFFCYGqLv-T
    256     276        6 IMVi-FLICWVPYA-VAFYIF
    285     305        7 PiFMTiPAFFAKSaAIYNPVI

#---------------------------------------
#---------------------------------------
#=======================================
#
# Sequence: OPSD_HUMAN     from: 1   to: 354
# HitCount: 7
#=======================================

  Start     End TransMem Sequence
     43      70        1 YMFLLIVLGFPINFLTLYVTVQHKKLRT
     71      98        2 PLNYILLNLAVADLFMVLGGFTSTLYTS
    112     140        3 LEGFFATLGGEIALWSLVVLAIERYVVVC
    148     176        4 FGENHAIMGVAFTWVMALACAAPPLAGWS
    201     229        5 ESFVIYMFVVHFTIPMIIIFFCYGQLVFT
    256     276        6 IMVIAFLICWVPYASVAFYIF
    285     305        7 PIFMTIPAFFAKSAAIYNPVI

#---------------------------------------
#---------------------------------------
#=======================================
#
# Sequence: OPSD_XENLA     from: 1   to: 354
# HitCount: 7
#=======================================

  Start     End TransMem Sequence
     43      70        1 YMFLLILLGLPINFMTLFVTIQHKKLRT
     71      98        2 PLNYILLNLVFANHFMVLCGFTVTMYTS
    112     140        3 IEGFFATLGGEVALWSLVVLAVERYIVVC
    148     176        4 FGENHAIMGVAFTWIMALSCAAPPLFGWS
    201     229        5 ESFVIYMFIVHFTIPLIVIFFCYGRLLCT
    256     276        6 IMVVFFLICWVPYAYVAFYIF
    285     305        7 PVFMTVPAFFAKSSAIYNPVI

#---------------------------------------
#---------------------------------------

#---------------------------------------
# Total_sequences: 2
# Total_length: 702
# Reported_sequences: 3
# Reported_hitcount: 21
#---------------------------------------

  Graphics File: tmap.ps

   [tmap results]

   A plot of the propensities to form the middle (solid line) and the end
   (dashed line) 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 -outfile option) gives a summary of
   these regions.

   The transmembrane regions for the complete alignment are given first,
   followed by the predictions for each individual sequence in the
   alignment.

Data files

   None.

Notes

   Two sets of transmembrane 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 aligned 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 corrections for strictly conserved charged residues are
   made.

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

References

    1. "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
                    sigcleave    Report on signal cleavage sites in a protein sequence

Author(s)

                    Original program by Bengt Persson and Patrick Argos.

                    This application was modified for inclusion in EMBOSS by Ian Longden
                    formerly at:
   Sanger           Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
                    CB10 1SA, UK.

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) not to the original author.

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

                    The graph y axis is not labelled. It is some kind of score, but we aer
                    not sure exactly how to describe it.
