Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid rep

Background: Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues – coevolution. Our goal is to find these coevolving residues. Results: We present six new methods for detecting coevolving residues. Among other things, we suggest measures that are variants of Mutual Information, and measures that use a multidimensional representation of each residue in order to capture the physico-chemical similarities between amino acids. We created a benchmarking system, in silico, able to evaluate these methods through a wide range of realistic conditions. Finally, we use the combination of different methods as a way of improving performance. Conclusion: Our best method (Row and Column Weighed Mutual Information) has an estimated accuracy increase of 63% over Mutual Information. Furthermore, we show that the combination of different methods is efficient, and that the methods are quite sensitive to the di...

• Type: Journal
• Year: 2007
• Where: ALMOB
• Authors: Rodrigo Gouveia-Oliveira, Anders Gorm Pedersen
• Keywords: ALMOB 2007, Amino Acids, Mutual Information, Phylogenetic Analysis