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tmap |
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 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.
The results are plotted on a graph and written to a text file.
% tmap opsd.msf -out tmap.res -graph cps Displays membrane spanning regions Created tmap.ps |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-sequences] seqset File containing a sequence alignment
-graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tekt, tek, none, data, xterm, png, gif)
[-outfile] report [*.tmap] Output report file name
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
-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 standard output
-filter boolean Read standard input, write 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. 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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequences] (Parameter 1) |
File containing a sequence alignment | Readable set of sequences | Required |
| -graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11 |
| [-outfile] (Parameter 2) |
Output report file name | Report output file | <*>.tmap |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
!!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
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########################################
# Program: tmap
# Rundate: Sun 15 Jul 2007 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 YMFLLIvLGxPINFlTLyVTvQHKKLRT
71 98 2 PLNYILLNLxxAdxFMVLxGFTxTlYTS
112 140 3 lEGFFATLGGEiALWSLVVLAiERYvVVC
148 176 4 FGENHAIMGVAFTWvMALaCAAPPLxGWS
201 229 5 ESFVIYMFvVHFTIPmIiIFFCYGqLvxT
256 276 6 IMVixFLICWVPYAxVAFYIF
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: 3
# Total_hitcount: 21
#---------------------------------------
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![[tmap results]](tmap.1.tmap.gif)
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.
| 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 |
This application was modified for inclusion in EMBOSS by
Ian Longden (il © sanger.ac.uk)
Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK.