tmap Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. 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:6.4.0.0 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 -sformat1 string Input sequence format -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: Fri 15 Jul 2011 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 Reports 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.