Evaluation of methods for the prediction of membrane spanning regions

Motivation: A variety of tools are available to predict the topology of tra nsmembrane proteins. To date no independent evaluation of the performance o f these tools has been published. A better understanding of the strengths a nd weaknesses of the different tools would guide both the biologist and the bioinformatician to make better predictions of membrane protein topology. Results: Here we present an evaluation of the performance of the currently best known and most widely used methods for the prediction of transmembrane regions in proteins. Our results show that TMHMM is currently the best per forming transmembrane prediction program.