Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes.

ABSTRACT:

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 sigma70 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 alpha subunit, and then optimally-separated patterns of -35 and -10 boxes, required for interaction with

SUBMITTER: Dekhtyar M 

PROVIDER: S-EPMC2412878 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature