0.01 Topology prediction of membrane proteins Heijne, Wallin, Claros, Deveaud, Schuerer von Heijne, G. (1992) Membrane Protein Structure Prediction: Hydrophobicity Analysis and the 'Positive Inside' Rule. J.Mol.Biol. 225, 487-494. Claros, M.G., and von Heijne, G. (1994) TopPred II: An Improved Software For Membrane Protein Structure Predictions. CABIOS 10, 685-686. Deveaud and Schuerer (Pasteur Institute) new implementation of the original toppred program, based on G. von Heijne algorithm. protein:2d structure toppred toppred perl "toppred" 0 query Sequence perl " $value" 8 10 graph_output Produce hydrophobicity graph image (-g) 1 topo_output Produce image of each topology (-t) perl ($value) ? "" : " -t none" 0 7 control Control options scale Hydrophobicity scale (-H) KD-scale KD-scale (Kyte and Doolittle) GVH-scale GVH-scale (Gunnar von Heijne) GES-scale GES-scale (Goldman Engelman Steitz) GES-scale perl ($value) ? " -H $value" : "" 1 organism Organism: eukaryot (default is prokaryot) (-e) perl ($value)? " -e " : "" 1 certain Upper cutoff (-c) 1.0 perl ($value && $value != $vdef)? " -c $value" : "" 2 putative Lower cutoff (-p) 0.6 perl ($value && $value != $vdef)? " -p $value" : "" 2 core Core window size: (-n) 10 perl ($value && $value != $vdef)? " -n $value" : "" 2 triangle Wedge window size: (-q) 5 perl ($value && $value != $vdef)? " -q $value" : "" 2 loop_length Critical loop length (-s) 60 perl ($value && $value != $vdef)? " -s $value" : "" 2 Segment_distance Critical transmembrane spacer (-d) 2 perl ($value && $value != $vdef)? " -d $value" : "" 2 output_options Output options outformat Output format (-O) perl ($value && $value ne $vdef) ? " -O $value" : "" 5 new New: new text output format html HTML old Old : output format of the old toppred implementation xml Xml new profile_format Hydrophobicity Profile file format png PNG output ps PostScript output ppm PPM output png perl ($graph_output) ? " -g $value" : " -g none" 7 graphicfiles *.ps *.ppm *.png *.html outputfiles *.hydro*