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Bioinformatics Advance Access originally published online on September 13, 2005
Bioinformatics 2005 21(22):4116-4124; doi:10.1093/bioinformatics/bti671
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org
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Using information theory to search for co-evolving residues in proteins

L. C. Martin 1, G. B. Gloor 2, S. D. Dunn 2 and L. M. Wahl 1,*

1Department of Applied Mathematics, University of Western Ontario London, Ontario, Canada N6A 5B7
2Department of Biochemistry, University of Western Ontario London, Ontario, Canada N6A 5B7

*To whom correspondence should be addressed.

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{at}uwo.ca

Supplementary information: http://www.biochem.uwo.ca/cgi-bin/CDD/index.cgi

Received on July 20, 2005; revised on September 2, 2005; accepted on September 8, 2005

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