Recognition of Eukaryotic Promoters Using a Genetic Algorithm Based on Iterative Discriminant Analysis

Issue title: 3rd International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002), June 2002, Novosibirsk, Russia

Article type: Research Article

Authors: Levitsky, Victor G. | Katokhin, Alexey V.

Affiliations: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

Abstract: A new approach to recognizing promoter regions of eukaryotic genes is proposed and illustrated by an example of Drosophila melanogaster. The essence of its novelty is in realizing the genetic algorithm to search for optimal partition of a promoter region into local nonoverlapping fragments and selection of the most significant dinucleotide frequencies for the fragments obtained. The method developed was applied to recognizing TATA-containing (TATA+) and DPE-containing (DPE+) promoters of Drosophila melanogaster genes. The program for promoter recognition is included into the GeneExpress system, section RegScan (http://wwwmgs.bionet.nsc.ru/mgs/programs/proga/).

Keywords: eukaryotic promoter recognition, genetic algorithml, discriminant analysis, promoter region partition, dinucleotide frequencies, TATA-containing promoters, DPE-containing promoters, nucleosome formation potentia

Journal: In Silico Biology, vol. 3, no. 1-2, pp. 81-87, 2003