Using ensemble classifier to identify membrane protein types

Summary.Predicting membrane protein type is both an important and challenging topic in current molecular and cellular biology. This is because knowledge of membrane protein type often provides useful clues for determining, or sheds light upon, the function of an uncharacterized membrane protein. With the explosion of newly-found protein sequences in the post-genomic era, it is in a great demand to develop a computational method for fast and reliably identifying the types of membrane proteins according to their primary sequences. In this paper, a novel classifier, the so-called “ensemble classifier”, was introduced. It is formed by fusing a set of nearest neighbor (NN) classifiers, each of which is defined in a different pseudo amino acid composition space. The type for a query protein is determined by the outcome of voting among these constituent individual classifiers. It was demonstrated through the self-consistency test, jackknife test, and independent dataset test that the ensemble classifier outperformed other existing classifiers widely used in biological literatures. It is anticipated that the idea of ensemble classifier can also be used to improve the prediction quality in classifying other attributes of proteins according to their sequences.