EMBOSS: tmap


Program 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 utilsing multiple sequence alignments J. Mol. Biol. 237, 182-192."

Usage

Here is a sample session with tmap.

  % tmap sw:opsd_human

click here for result

Command line arguments

   Mandatory qualifiers:
  [-msf]               seqset     File containing a sequence alignment
   -graph              xygraph    Graph type

   Optional qualifiers:
   -outfile            outfile    Output file name

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default
[-msf]
(Parameter 1)
File containing a sequence alignment Readable 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 EMBOSS_GRAPHICS value, or x11
Optional qualifiers Allowed values Default
-outfile Output file name Output file tmap.res
Advanced qualifiers Allowed values Default
(none)

Input file format

Any protein sequence USA for one or more aligned sequences.

Output file format

.ps file if postscipt output requested.

Data files

Notes

References

"Persson, B. & Argos, P. (1994) Prediction of transmembrane segments in proteins utilsing multiple sequence alignments J. Mol. Biol. 237, 182-192."

Warnings

Diagnostic Error Messages

Exit status

0 if successfull.

Known bugs

See also

Program nameDescription
antigenicFinds antigenic sites in proteins
diffseqFind differences (SNPs) between nearly identical sequences
dotmatcherDisplays a thresholded dotplot of two sequences
dotpathDisplays a non-overlapping wordmatch dotplot of two sequences
dottupDisplays a wordmatch dotplot of two sequences
garnierPredicts protein secondary structure
helixturnhelixReport nucleic acid binding motifs
oddcompFinds protein sequence regions with a biased composition
pepcoilPredicts coiled coil regions
polydotDisplays all-against-all dotplots of a set of sequences
pscanScans proteins using PRINTS
showseqDisplay a sequence with features, translation etc
sigcleaveReports protein signal cleavage sites

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) Informatics Division, The Sanger Centre, 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