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

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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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Correspondence to Chris Hemmerich.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Hemmerich, C., Kim, S. A Study of Residue Correlation within Protein Sequences and Its Application to Sequence Classification. J Bioinform Sys Biology 2007, 87356 (2007) doi:10.1155/2007/87356

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Keywords

  • Protein Sequence
  • Mutual Information
  • Long Range
  • System Biology
  • Modeling Power