Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress

Background: In our previous studies, we found that the sites in prokaryotic genomes which are most susceptible to duplex destabilization under the negative superhelical stresses that occur in vivo are statistically highly significantly associated with intergenic regions that are known or inferred to contain promoters. In this report we investigate how this structural property, either alone or together with other structural and sequence attributes, may be used to search prokaryotic genomes for promoters. Results: We show that the propensity for stress-induced DNA duplex destabilization (SIDD) is closely associated with specific promoter regions. The extent of destabilization in promotercontaining regions is found to be bimodally distributed. When compared with DNA curvature, deformability, thermostability or sequence motif scores within the -10 region, SIDD is found to be the most informative DNA property regarding promoter locations in the E. coli K12 genome. SIDD properties alone per...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Huiquan Wang, Craig J. Benham
• Keywords: BMCBI 2006, Prokaryotic Genomes, Promoter, Promoter Regions