A novel method for predicting transmembrane segment
in proteins based on a statistical analysis of the SwissProt database
Pasquier, C., Promponas, V.J., Palaios, G.A., Hamodrakas, J.S. and Hamodrakas, S.J.
Department of Cell Biology and Biophysics,
Faculty of Biology, University of Athens
Panepistimiopolis, Kouponia, Athens 15701, Greece
PRED-TMR is a novel method that predicts transmembrane domains in proteins
using solely information contained in the sequence itself. The algorithm
refines a standard hydrophobicity analysis with a detection of potential
termini ("edges", starts and ends) of transmembrane regions. This allows
both to discard highly hydrophobic regions not delimited by clear start
and end configurations and to confirm putative transmembrane segments not
distinguishable by their hydrophobic composition.
The accuracy obtained on a test set of 101 non homologous transmembranes
proteins with reliable topologies compares well with that of other popular
existing methods. Only a slight decrease in prediction accuracy was observed
when the algorithm was applied to all transmembrane proteins of the SwissProt
database (release 35).
The algorithm is described in :
Pasquier C, Promponas VJ, Palaios GA, Hamodrakas JS, Hamodrakas SJ:
A novel method for predicting transmembrane segments in proteins based on a
statistical analysis of the SwissProt database: the PRED-TMR algorithm.
Protein Eng 1999 May;12(5):381-5