aligning sequences by minimum description length调整最小描述长度的序列.pdfVIP

Hindawi Publishing Corporation EURASIP Journal on Bioinformatics and Systems Biology Volume 2007, Article ID 72936, 14 pages doi:10.1155/2007/72936 Research Article Aligning Sequences by Minimum Description Length John S. Conery Department of Computer and Information Science, University of Oregon, Eugene, OR 97403, USA Received 26 February 2007; Revised 6 August 2007; Accepted 16 November 2007 ¨ Recommended by Peter Grunwald This paper presents a new information theoretic framework for aligning sequences in bioinformatics. A transmitter compresses a set of sequences by constructing a regular expression that describes the regions of similarity in the sequences. To retrieve the original set of sequences, a receiver generates all strings that match the expression. An alignment algorithm uses minimum de- scription length to encode and explore alternative expressions; the expression with the shortest encoding provides the best overall alignment. When two substrings contain letters that are similar according to a substitution matrix, a code length function based on conditional probabilities defined by the matrix will encode the substrings with fewer bits. In one experiment, alignments produced with this new method were found to be comparable to alignments from CLUSTALW. A second experiment measured the accuracy of the new method on pairwise alignments of sequences from the BAliBASE alignment benchmark. Copyright © 2007 John S. Conery. 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 represent the sequences. If there are se