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Research Article
Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
Article first published online: 14 MAY 2004
DOI: 10.1002/prot.20098
Copyright © 2004 Wiley-Liss, Inc.
Issue
1097-0134/asset/cover.gif?v=1&s=d817e79b67ba6cacf8bdcce1a819c04de300a7e3 "Proteins: Structure, Function, and Bioinformatics")
Proteins: Structure, Function, and Bioinformatics
Volume 56, Issue 2, pages 211–221, 1 August 2004
Additional Information
How to Cite
Fodor, A. A. and Aldrich, R. W. (2004), Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins: Structure, Function, and Bioinformatics, 56: 211–221. doi: 10.1002/prot.20098
Publication History
- Issue published online: 11 JUN 2004
- Article first published online: 14 MAY 2004
- Manuscript Accepted: 11 DEC 2003
- Manuscript Revised: 4 DEC 2003
- Manuscript Received: 24 JUL 2003
Funded by
- Mathers Foundation
Keywords:
- structure–function;
- protein engineering;
- genomics;
- evolution;
- Pfam;
- Protein Data Bank;
- covariance
Abstract
It has long been argued that algorithms that find correlated mutations in multiple sequence alignments can be used to find structurally or functionally important residues in proteins. We examined the properties of four different methods for detecting these correlated mutations. On both simple, artificial alignments and real alignments from the Pfam database, we found a surprising lack of agreement between the four correlated mutation methods. We argue that these differences are caused in part by differing sensitivities to background conservation. Correlated mutation algorithms can be envisioned as “filters” of background conservation with each algorithm searching for correlated mutations that occur at a different background conservation frequency. Proteins 2004. © 2004 Wiley-Liss, Inc.