Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs.

ABSTRACT:

Background

In bacteria, sigma factors and other transcriptional regulatory proteins recognize DNA patterns upstream of their target genes and interact with RNA polymerase to control transcription. As a consequence of evolution, DNA sequences recognized by transcription factors are thought to be enriched in intergenic regions (IRs) and depleted from coding regions of prokaryotic genomes.

Results

In this work, we report that genomic distribution of transcription factors binding sites is biased towards IRs, and that this bias is conserved amongst bacterial species. We further take advantage of this observation to develop an algorithm that can efficiently identify promoter boxes by a distribution-dependent approach rather than a direct sequence comparison approach. This strategy

SUBMITTER: Jacques PE 

PROVIDER: S-EPMC1615881 | biostudies-literature | 2006 Oct

REPOSITORIES: biostudies-literature