IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions.

ABSTRACT:

Motivation

During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches.

Results

We introduce INTARNA, a new general and fast approach to the prediction of RNA-RNA interactions incorpo

SUBMITTER: Busch A 

PROVIDER: S-EPMC2639303 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature