Transcription factor binding site recognition by regularity matrices based on the natural classification method

Authors:
E. E. Vityaev;K. A. Lapardin;I. V. Khomicheva;A. L. Proskura
Affiliations:
(Correspd. Fax: +7 383 333 25 98/ E-mail: vityaev@bionet.nsc.ru) Institute of Mathematics SB RAS, Novosibirsk, Russia and Novosibirsk State University, Novosibirsk, Russia;Novosibirsk State University, Novosibirsk, Russia;Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia;Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Venue:
Intelligent Data Analysis - New Methods in Bioinformatics Presented at the Fifth International Conference on Bioinformatics of Genome Regulation and Structure
Year:
2008

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Abstract

A principally new approach to the classifications of nucleotide sequences based on the "natural" classification concept is proposed. As a result of "natural" classification of the nucleotide sequences, we obtain regularity matrices, where nucleotides are interconnected by regularities. Method, algorithm and software system DNANatClass for performing the "natural" classification have been developed. Experimental results comparing weight matrices with regularity matrices are presented. In this experiment, site recognition by regularity matrices appears to be more accurate than by weight matrixes.