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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:6.6.0.0
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
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-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: Mon 15 Jul 2013 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.
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