Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake.

ABSTRACT:

Background

In many prokaryotes, transcription of DNA to RNA is terminated by a thymine-rich stretch of DNA following a hairpin loop. Detecting such Rho-independent transcription terminators can shed light on the organization of bacterial genomes and can improve genome annotation. Previous computational methods to predict Rho-independent terminators have been slow or limited in the organisms they consider.

Results

We describe TransTermHP, a new computational method to rapidly and accurately detect Rho-independent transcription terminators. We predict the locations of terminators in 343 prokaryotic genomes, representing the largest collection of predictions available. In Bacillus subtilis, we can detect 93% of known terminators with a false positive rate of just 6%, comparable

SUBMITTER: Kingsford CL 

PROVIDER: S-EPMC1852404 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature