Proceedings of the twelfth international conference on 3D web technology
EURASIP Journal on Bioinformatics and Systems Biology
Co-evolution and Information Signals in Biological Sequences
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
Research article: Estimating sufficient statistics in co-evolutionary analysis by mutual information
Computational Biology and Chemistry
Physicochemical correlation between amino acid sites in short sequences under selective pressure
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Co-evolution and information signals in biological sequences
Theoretical Computer Science
Computational Biology and Chemistry
Information-theoretic analysis of molecular (co)evolution using graphics processing units
Proceedings of the 3rd international workshop on Emerging computational methods for the life sciences
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Motivation: Some functionally important protein residues are easily detected since they correspond to conserved columns in a multiple sequence alignment (MSA). However important residues may also mutate, with compensatory mutations occurring elsewhere in the protein, which serve to preserve or restore functionality. It is difficult to distinguish these co-evolving sites from other non-conserved sites. Results: We used Mutual Information (MI) to identify co-evolving positions. Using in silico evolved MSAs, we examined the effects of the number of sequences, the size of amino acid alphabet and the mutation rate on two sources of background MI: finite sample size effects and phylogenetic influence. We then assessed the performance of various normalizations of MI in enhancing detection of co-evolving positions and found that normalization by the pair entropy was optimal. Real protein alignments were analyzed and co-evolving isolated pairs were often found to be in contact with each other. Availability: All data and program files can be found at http://www.biochem.uwo.ca/cgi-bin/CDD/index.cgi Contact: lwahl@uwo.ca Supplementary information: http://www.biochem.uwo.ca/cgi-bin/CDD/index.cgi