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
algorithm
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.
gmail.com