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Bioinformatics Advance Access published online on September 13, 2005
Bioinformatics, 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@oxfordjournals.org
Received July 20, 2005
Revised September 2, 2005
Accepted September 8, 2005

Article

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*

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

* To whom correspondence should be addressed.
L. M. Wahl, E-mail: lwahl{at}uwo.ca


  Abstract

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 normalizing 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.


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