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.
