EMBOSS: tmap

| 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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequences] (Parameter 1) | seqset | File containing a protein sequence alignment | Readable set of sequences | Required
-graph | xygraph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg | EMBOSS_GRAPHICS value, or x11
[-outfile] (Parameter 2) | report | Output report file name | (default -rformat seqtable) | <*>.tmap
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequences" associated seqset qualifiers
-sbegin1 -sbegin_sequences | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequences | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequences | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequences | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequences | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequences | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequences | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequences | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequences | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_sequences | string | Input sequence format | Any string |
-iquery1 -iquery_sequences | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequences | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequences | string | Database name | Any string |
-sid1 -sid_sequences | string | Entryname | Any string |
-ufo1 -ufo_sequences | string | UFO features | Any string |
-fformat1 -fformat_sequences | string | Features format | Any string |
-fopenfile1 -fopenfile_sequences | string | Features file name | Any string |
"-graph" associated xygraph qualifiers
-gprompt | boolean | Graph prompting | Boolean value Yes/No | N
-gdesc | string | Graph description | Any string |
-gtitle | string | Graph title | Any string |
-gsubtitle | string | Graph subtitle | Any string |
-gxtitle | string | Graph x axis title | Any string | Residue number
-gytitle | string | Graph y axis title | Any string |
-goutfile | string | Output file for non interactive displays | Any string | tmap
-gdirectory | string | Output directory | Any string |
"-outfile" associated report qualifiers
-rformat2 -rformat_outfile | string | Report format | Any string | seqtable
-rname2 -rname_outfile | string | Base file name | Any string |
-rextension2 -rextension_outfile | string | File name extension | Any string |
-rdirectory2 -rdirectory_outfile | string | Output directory | Any string |
-raccshow2 -raccshow_outfile | boolean | Show accession number in the report | Boolean value Yes/No | N
-rdesshow2 -rdesshow_outfile | boolean | Show description in the report | Boolean value Yes/No | N
-rscoreshow2 -rscoreshow_outfile | boolean | Show the score in the report | Boolean value Yes/No | Y
-rstrandshow2 -rstrandshow_outfile | boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y
-rusashow2 -rusashow_outfile | boolean | Show the full USA in the report | Boolean value Yes/No | N
-rmaxall2 -rmaxall_outfile | integer | Maximum total hits to report | Any integer value | 0
-rmaxseq2 -rmaxseq_outfile | integer | Maximum hits to report for one sequence | Any integer value | 0
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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

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 © 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.