Open Access

A Study of Residue Correlation within Protein Sequences and Its Application to Sequence Classification

EURASIP Journal on Bioinformatics and Systems Biology20072007:87356

https://doi.org/10.1155/2007/87356

Received: 28 February 2007

Accepted: 31 July 2007

Published: 10 September 2007

Abstract

We investigate methods of estimating residue correlation within protein sequences. We begin by using mutual information (MI) of adjacent residues, and improve our methodology by defining the mutual information vector (MIV) to estimate long range correlations between nonadjacent residues. We also consider correlation based on residue hydropathy rather than protein-specific interactions. Finally, in experiments of family classification tests, the modeling power of MIV was shown to be significantly better than the classic MI method, reaching the level where proteins can be classified without alignment information.

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Authors’ Affiliations

(1)
Center For Genomics and Bioinformatics, Indiana University
(2)
School of Informatics, Center for Genomics and Bioinformatics, Indiana University

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Copyright

© C. Hemmerich and S. Kim. 2007

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.