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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 alignged 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 correctionbs 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 sw:opsd_human -out tmap.resclick here for result
Mandatory qualifiers: [-msf] seqset File containing a sequence alignment -graph xygraph Graph type Optional qualifiers: -outfile outfile Output file name Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
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, png | EMBOSS_GRAPHICS value, or x11 |
Optional qualifiers | Allowed values | Default | |
-outfile | Output file name | Output file | tmap.res |
Advanced qualifiers | Allowed values | Default | |
(none) |
Bars are displayed in the plot above the regions predicted as being most likely to form transmembrane regions.
The text file (specified by the -output option) gives a summary of these regions. The text file produced by the above example is:
Program TMAP, version 46, to predict transmembrane segments from .msf file. The program reads a multiple alignment file of the GCG multiple sequence format and predicts membrane-spanning regions according to the algorithm in Persson & Argos (1994), J. Mol. Biol. 237, 182-192. RESULTS from program TMAP, edition 46' Numbers give: a) number of transmembrane segment b) start of TM segment (alignment position / residue number) c) end of TM segment (alignment position / residue number) d) length of TM segment within parentheses PREDICTED TRANSMEMBRANE SEGMENTS FOR ALIGNMENT TM 1: 43 - 69 (27.0) TM 2: 73 - 97 (25.0) TM 3: 112 - 140 (29.0) TM 4: 148 - 176 (29.0) TM 5: 201 - 229 (29.0) TM 6: 255 - 275 (21.0) TM 7: 282 - 302 (21.0) PREDICTED TRANSMEMBRANE SEGMENTS FOR PROTEIN OPSD_HUMAN TM 1: 43 - 69 (27) TM 2: 73 - 97 (25) TM 3: 112 - 140 (29) TM 4: 148 - 176 (29) TM 5: 201 - 229 (29) TM 6: 255 - 275 (21) TM 7: 282 - 302 (21)
The transmembrane regions for the complete alignment are given first, followed by the predictions for each individual sequence in the alignment. (In the example above there is only 1 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) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.