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)

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

Program name	Description
antigenic	Finds antigenic sites in proteins
diffseq	Find differences (SNPs) between nearly identical sequences
dotmatcher	Displays a thresholded dotplot of two sequences
dotpath	Displays a non-overlapping wordmatch dotplot of two sequences
dottup	Displays a wordmatch dotplot of two sequences
garnier	Predicts protein secondary structure
helixturnhelix	Report nucleic acid binding motifs
oddcomp	Finds protein sequence regions with a biased composition
pepcoil	Predicts coiled coil regions
polydot	Displays all-against-all dotplots of a set of sequences
pscan	Scans proteins using PRINTS
showseq	Display a sequence with features, translation etc
sigcleave	Reports 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.