TMAP
TMAP. Predicts transmembrane segments in proteins; 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. Drawtree interactively plots an unrooted tree diagram, with many options including orientation of tree and branches, label sizes and angles, margin sizes.
If you use this tool, please cite Persson, B. and Argos, P. (1994) "Prediction of transmembrane segments in proteins utilising multiple sequence alignments" J. Mol. Biol. 237, 182-192.
Manual: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/tmap.html
INPUT = Protein Sequences in GCG format.
TEST INPUT FILES
Input file: tmap1.txt
TEST OUTPUT FILES
Output file: tmap.1.png