toppred

transmembrane topology prediction

Toppred is a program to determine the topology of a transmembrane protein based on G. von Heijne algorithm. Each sequence from seq data in fasta format is processed, and toppred generate the Hydrophobycity profile of the sequence, and the corresponding hydrophobycities values in the file sequence-ID.hydro. Furthermore, the predicted topologies are represented as png images. Each topology is stored in file sequence-ID-number.png The hydrophobicity profile is computed using a window formed by a core rectangular window of size n, flanked by 2 triangular windows of size q. NB rectangular and triangular mean that the ponderation values inside those windows are respectively constant and variable. This program is a new implementation of the original toppred program, based on G. von Heijne algorithm