Evaluation of fuzzy measures in profile hidden Markov models for protein sequences

Abstract

In biological problems such as protein sequence family identification and profile building the additive hypothesis of the probability measure is not well suited for modeling HMM based profiles because of a high degree of interdependency among homologous sequences of the same family. Fuzzy measure theory which is an extension of the classical additive theory is obtained by replacing the additive requirement of classical measures with weaker properties of monotonicity, continuity and semi-continuity. The strong correlations and the sequence preference involved in the protein structures make fuzzy measure architecture based models as suitable candidates for building profiles of a given family since fuzzy measures can handle uncertainties better than classical methods. In this paper we investigate the different measures(S-decomposable, λ and belief measures) of fuzzy measure theory for building profile models of protein sequence problems. The proposed fuzzy measure models have been tested on globin and kinase families. The results obtained from the fuzzy measure models establish the superiority of fuzzy measure theory compared to classical probability measures for biological sequence problems. © Springer-Verlag Berlin Heidelberg 2005.