- Article -
| In Silico Biology 3, 0008 (2003); ©2003, Bioinformation Systems e.V. |
Recognition of eukaryotic promoters using a genetic algorithm based on iterative discriminant analysis
Victor G. Levitsky* and Alexey V. Katokhin
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Email: levitsky@bionet.nsc.ru
* corresponding author
Edited by P. Bucher; received October 04, 2002; revised and accepted February 18, 2003; published February 27, 2003
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/).
Key words: eukaryotic promoter recognition, genetic algorithm, discriminant analysis, promoter region partition, dinucleotide frequencies, TATA-containing promoters, DPE-containing promoters, nucleosome formation potential