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

ABSTRACT:

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 promoter-containing regions is found to be bimodally distributed. When compared with DNA curvature, d

SUBMITTER: Wang H 

PROVIDER: S-EPMC1468432 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature