Manual of the HTP database

Filtering transmembrane proteins

Eight prediction methods have been tested to filter transmembrane proteins, i.e. determining whether a sequence codes a transmembrane protein or a non-transmembrane one. These methods are Memsat, Octopus, Philius, Phobius, Pro-TMHMM Scampi-single, Scampi-msa and TMHMM. They were executed on preprocessed sequences, i.e. after removing transit and/or signal peptides from the query sequences. As none of these method’s accuracies were as high as desired, a simple consensus approach were utilized to increase the prediction accuracy. Dozens of combinations of these approaches and parameters were tested and the best was chosen as the final consensus algorithm. The highest accuracy was reached, when three specific methods were used for filtering, namely Phobius, Scampi-single, TMHMM, and at least two of these predicted at least one membrane region.