Substitution Matrices and Mutual Information Approaches to Modeling Evolution

Abstract. Substitution matrices are at the heart of Bioinformatics: sequence alignment, database search, phylogenetic inference, protein family classication are based on Blosum, Pam, JTT, mtREV24 and other matrices. These matrices provide means of computing models of evolution and assessing the statistical relationships amongst sequences. This paper reports two results; rst we show how Bayesian and grid settings can be used to derive novel specic substitution matrices for sh and insects and we discuss their performances with respect to standard amino acid replacement matrices. Then we discuss a novel application of these matrices: a renement of the mutual information formula applied to amino acid alignments by incorporating a substitution matrix into the calculation of the mutual information. We show that dierent substitution matrices provide qualitatively dierent mutual information results and that the new algorithm allows the derivation of better estimates of the similarity al...

• Type: Conference
• Year: 2009
• Where: LION
• Authors: Stephan Kitchovitch, Yuedong Song, Richard C. van der Wath, Pietro Liò
• Keywords: LION 2009, Mutual Information, Optimization, Specic Substitution Matrices, Substitution Matrices