Welcome to hPATM
The hPATM algorithm, based on a heuristic transformation of the original global pairwise and local pairwise alignment algorithms, offers objective alignments for transmembrane protein sequences. hPATM takes advantage of the information offered by the knowledge of the position of transmembrane segmets, by experiment or prediction. The heuristic approach may reveal similarities between diverge sequences with low percentages of identity and similarity. The produced alignments, based on common structural scaffolds derived by the transmembrane segments of the sequence, can be used to spot conserved non-transmembrane segments or as a basis for the production of 3-D models via homology modelling.
About the hPATM
The hPAFAG algorithm is based on the heuristic transformation of the Needleman & Wunsch and Smith & Waterman algorithms, featuring affine gap penalties. The heuristic transformation is based on two extra features:
- a heuristic "bonus", added to the score when two aminoacids that belong to transmembrane segmens are aligned.
- a heuristic gap penalty, substracted from the score when a gap is opened in a transmembrane segment.
*: not by force, but by more "strict" alignment
About the hPATM web service
This web server offers a friendly interface for the hPATM command line version. The algorithm was implemented in PERL and the source code of the command line version is availaible on request by the authors.