Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes

Background: Bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. This difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. Results: We describe a new triad pattern algorithm that predicts strong promoter candidates in annotated bacterial genomes by matching specific patterns for the group I 70 factors of Escherichia coli RNA polymerase. It detects promoter-specific motifs by consecutively matching three patterns, consisting of an UP-element, required for interaction with the subunit, and then optimallyseparated patterns of -35 and -10 boxes, required for interaction with the 70 subunit of RNA polymerase. Analysis of 43 bacterial genomes revealed that the frequency of candidate sequences depends on the A+T content of the DNA under examination. The accuracy of in silico prediction was experi...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Michael Dekhtyar, Amelie Morin, Vehary Sakanyan
• Keywords: Bacterial Genomes, BMCBI 2008, Promoter, Strong Promoters