a study of residue correlation within protein sequences and its application to sequence classification内残留的研究相关蛋白质序列及其序列分类中的应用.pdfVIP

Hindawi Publishing Corporation EURASIP Journal on Bioinformatics and Systems Biology Volume 2007, Article ID 87356, 9 pages doi:10.1155/2007/87356 Research Article A Study of Residue Correlation within Protein Sequences and Its Application to Sequence Classification Chris Hemmerich1 and Sun Kim2 1 Center For Genomics and Bioinformatics, Indiana University, 1001 E. 3rd Street, Bloomington 47405-3700, India 2 School of Informatics, Center for Genomics and Bioinformatics, Indiana University, 901 E. 10th Street, Bloomington 47408-3912, India Received 28 February 2007; Revised 22 June 2007; Accepted 31 July 2007 Recommended by Juho Rousu 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. Copyright © 2007 C. Hemmerich and S. Kim. 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. 1. INTRODUCTION tein structure. To investigate this question, we used the fam- ily and sequence alignment information from Pfam-A [4]. To A protein can be viewed as a string