heuristic pairwise alignment for
          transmembrane proteins.

Zografos L.A., Promponas V.J., Hamodrakas S.J.,
Heuristic Pairwise alignment for Transmembrane Proteins.
Department of Cell Biology and Biophysics,
Faculty of Biology, University of Athens,
Panepistimiopolis, Athens 15701, Greece

Relative Tools

You can use PRED-TMR
to predict alpha-helical or PRED-TMBB to predict beta-barrel transmembrane segments in your sequences

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:

This way transmembrane segments are anchored* together, allowing the pairwise alignment to focus on non-transmembrane segments.

*: 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.