An evolutionary approach for motif discovery and transmembrane protein classification

Abstract

Proteins can be grouped into families according to their biological functions. This paper presents a system, named GAMBIT, which discovers motifs (particular sequences of amino acids) that occur very often in proteins of a given family but rarely occur in proteins of other families. These motifs are used to classify unknown proteins, that is, to predict their function by analyzing the primary structure. To search for motifs in proteins, we developed a GA with specially tailored operators for the problem. GAMBIT was compared with MEME, a web tool for finding motifs in the TransMembrane Protein DataBase. Motifs found by both methods were used to build a decision tree and classification rules, using, respectively, C4.5 and Prism algorithms. Motifs found by GAMBIT led to significantly better results, when compared with those found by MEME, using both classification algorithms. © Springer-Verlag Berlin Heidelberg 2005.