RNApredator: Fast accessibility-Based Prediction of sRNA targets

RNApredator: Fast accessibility-Based Prediction of sRNA targets

Abstract

Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5′-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcript and/or its ability to be translated. Here, we present RNApredator, a web server for the prediction of sRNA targets. The user can choose from a set of over 2155 genomes and plasmids from 1183 bacterial species. RNApredator then uses a dynamic programming approach, RNAplex, to compute putative targets. Compared to web servers with a similar task, RNApredator takes the accessibility of the target during the target search into account, improving the specificity of the predictions. Furthermore, enrichment in Gene Ontology terms, cellular pathways as well as changes in accessibilities along the target sequence can be done in fully automated post-processing steps. The predictive performance of the underlying dynamic programming approach RNAplex is similar to that of more complex methods, but needs at least three orders of magnitude less time to complete. RNApredator is available at http://rna.tbi.univie.ac.at/RNApredator.

Grafik Top
Authors
  • Eggenhofer, Florian
  • Tafer, Hakim
  • Stadler, Peter F.
  • Hofacker, Ivo L.
Grafik Top
Shortfacts
Category
Journal Paper
Divisions
Bioinformatics and Computational Biology
Subjects
Angewandte Informatik Sonstiges
Journal or Publication Title
Nucleic Acids Research 2011
Publisher
Oxford University Press
Page Range
W149-W154
Number
S2
Volume
39
Date
2011
Export
Grafik Top