
                                   tmap 



Function

   Displays membrane spanning regions

Description

   This program predicts transmembrane segments in proteins, 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."

   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.

Usage

   Here is a sample session with tmap


% tmap tsw:opsd_human -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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     File containing a sequence alignment
   -graph              xygraph    Graph type

   Additional (Optional) qualifiers:
   -outfile            report     Output report file name

   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
   -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
   -rformat             string     Report format
   -rname               string     Base file name
   -rextension          string     File name extension
   -rdirectory          string     Output directory
   -raccshow            boolean    Show accession number in the report
   -rdesshow            boolean    Show description in the report
   -rscoreshow          boolean    Show the score in the report
   -rusashow            boolean    Show the full USA in the report

   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 deaths


   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
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png, xml EMBOSS_GRAPHICS value, or x11
   Additional (Optional) qualifiers Allowed values Default
   -outfile Output report file name Report output file
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   tmap reads a protein sequence USA for one or more aligned sequences.

  Input files for usage example

   'tsw:opsd_human' is a sequence entry in the example protein database
   'tsw'

  Database entry: tsw:opsd_human

ID   OPSD_HUMAN     STANDARD;      PRT;   348 AA.
AC   P08100; Q16414;
DT   01-AUG-1988 (Rel. 08, Created)
DT   01-AUG-1988 (Rel. 08, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   RHODOPSIN.
GN   RHO.
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE; 84272729.
RA   NATHANS J., HOGNESS D.S.;
RT   "Isolation and nucleotide sequence of the gene encoding human
RT   rhodopsin.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
RN   [2]
RP   SEQUENCE OF 1-120 FROM N.A.
RA   BENNETT J., BELLER B., SUN D., KARIKO K.;
RL   Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   REVIEW ON ADRP VARIANTS.
RX   MEDLINE; 94004905.
RA   AL-MAGHTHEH M., GREGORY C., INGLEHEARN C., HARDCASTLE A.,
RA   BHATTACHARYA S.;
RT   "Rhodopsin mutations in autosomal dominant retinitis pigmentosa.";
RL   Hum. Mutat. 2:249-255(1993).
RN   [4]
RP   VARIANT ADRP HIS-23.
RX   MEDLINE; 90136922.
RA   DRYJA T.P., MCGEE T.L., REICHEI E., HAHN L.B., COWLEY G.S.,
RA   YANDELL D.W., SANDBERG M.A., BERSON E.L.;
RT   "A point mutation of the rhodopsin gene in one form of retinitis
RT   pigmentosa.";
RL   Nature 343:364-366(1990).
RN   [5]
RP   VARIANTS ADRP.
RX   MEDLINE; 91051574.
RA   FARRAR G.J., KENNA P., REDMOND R., MCWILLIAM P., BRADLEY D.G.,
RA   HUMPHRIES M.M., SHARP E.M., INGLEHEARN C.F., BASHIR R., JAY M.,
RA   WATTY A., LUDWIG M., SCHINZEL A., SAMANNS C., GAL A.,
RA   BHATTACHARYA S.S., HUMPHRIES P.;
RT   "Autosomal dominant retinitis pigmentosa: absence of the rhodopsin
RT   proline-->histidine substitution (codon 23) in pedigrees from
RT   Europe.";
RL   Am. J. Hum. Genet. 47:941-945(1990).
RN   [6]
RP   VARIANTS ADRP HIS-23; ARG-58; LEU-347 AND SER-347.
RX   MEDLINE; 91015273.


  [Part of this file has been deleted for brevity]

FT                                /FTId=VAR_004816.
FT   VARIANT     209    209       V -> M (EFFECT NOT KNOWN).
FT                                /FTId=VAR_004817.
FT   VARIANT     211    211       H -> P (IN ADRP).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -> R (IN ADRP).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -> K (IN ADRP).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -> C (IN ADRP).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -> R (IN ADRP).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       MISSING (IN ADRP).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       MISSING (IN ADRP).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -> L (IN ADRP).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -> R (IN ADRP).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -> E (IN CSNB4).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -> E (IN ADRP).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -> R (IN ADRP).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -> M (IN ADRP).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -> L (IN ADRP).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -> M (IN ADRP).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -> A (IN ADRP).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -> L (IN ADRP; COMMON VARIANT).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -> Q (IN ADRP).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -> R (IN ADRP).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (IN ADRP).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38892 MW;  07443BEA CRC32;
     MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
     VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
     GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
     EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
     ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
     YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//

Output file format

  Output files for usage example

  File: tmap.res

########################################
# Program: tmap
# Rundate: Thu Jul 15 2004 12:00:00
# Report_format: seqtable
# Report_file: tmap.res
########################################

#=======================================
#
# Sequence: Consensus     from: 1   to: 348
# HitCount: 7
#=======================================

  Start     End TransMem Sequence
     43      69        1 YMFLLIVLGFPINFLTLYVTVQHKKLR
     73      97        2 NYILLNLAVADLFMVLGGFTSTLYT
    112     140        3 LEGFFATLGGEIALWSLVVLAIERYVVVC
    148     176        4 FGENHAIMGVAFTWVMALACAAPPLAGWS
    201     229        5 ESFVIYMFVVHFTIPMIIIFFCYGQLVFT
    255     275        6 IIMVIAFLICWVPYASVAFYI
    282     302        7 NFGPIFMTIPAFFAKSAAIYN

#---------------------------------------
#---------------------------------------
#=======================================
#
# Sequence: OPSD_HUMAN     from: 1   to: 348
# HitCount: 7
#=======================================

  Start     End TransMem Sequence
     43      69        1 YMFLLIVLGFPINFLTLYVTVQHKKLR
     73      97        2 NYILLNLAVADLFMVLGGFTSTLYT
    112     140        3 LEGFFATLGGEIALWSLVVLAIERYVVVC
    148     176        4 FGENHAIMGVAFTWVMALACAAPPLAGWS
    201     229        5 ESFVIYMFVVHFTIPMIIIFFCYGQLVFT
    255     275        6 IIMVIAFLICWVPYASVAFYI
    282     302        7 NFGPIFMTIPAFFAKSAAIYN

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

  Graphics File: tmap.ps

   [tmap results]

   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 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. (There is only one sequence in the example alignment.)

Data files

   None.

Notes

   None.

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
   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

Author(s)

   Original program by Bengt Persson and Patrick Argos.

   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.

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.
