A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm

We present a novel method that predicts transmembrane domains in proteins u sing solely information contained in the sequence itself. The PRED-TMR algo rithm described, refines a standard hydrophobicity analysis with a detectio n of potential termini ('edges', starts and ends) of transmembrane regions. This allows one both to discard highly hydrophobic regions not delimited b y 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 transmembrane proteins with r eliable topologies compares well with that of other popular existing method s. Only a slight decrease in prediction accuracy was observed when the algo rithm was applied to all transmembrane proteins of the SwissProt database ( release 35), A WWW server running the PRED-TMR algorithm is available at ht tp://o2.db.uoa.gr/PRED-TMR/.