uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
AntisenseRNA: fast, specific target prediction for bacterial sRNAs through models of interaction and evolutionary conservation
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Small regulatory RNAs (sRNAs) are ubiquitously present in many different bacteria and are often conserved in closely related species. The majority of the sRNAs acts as antisense RNAs via basepairing to target mRNAs and mediates up- or down-regulation. This involves effects on translation and/or mRNA stability. Since antisense-target RNA interaction sites are often short and non-contiguous, prediction of targets is a non-trivial task. Thus, most sRNA have not yet been assigned to specific target genes, and this motivates a need for computational target prediction programs. Available programs use criteria such as, for instance, a "seed" antisense-target interaction and the structural accessibility of the interaction site to indentify sRNA targets. So far, the realization that RNA/RNA interaction is a hierarchical multi-step process has not been incorporated into algorithms, and neither has conservation of interactions between related species. We have designed a target prediction program, AntisenseRNA, which considers the interaction as a multistep process, in which the intramolecular structure of the two RNAs and the phylogenetic conservation of basepairs are taken into account. AntisenseRNA successfully identifies most of the experimentally validated sRNA targets in Escherichia coli and predicts their interaction sites with high specificity and sensitivity. AntisenseRNA is about ten times faster than its best competitor programs, suggesting it to be a good choice for identification of new targets for sRNAs.

National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-131166OAI: oai:DiVA.org:uu-131166DiVA: diva2:353382
Available from: 2010-09-27 Created: 2010-09-26 Last updated: 2014-05-28

Open Access in DiVA

No full text

Search in DiVA

By author/editor
Reimegård, JohanWagner, Gerhart Eduard Heinrich
Natural Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 202 hits
ReferencesLink to record
Permanent link

Direct link