biRNA: fast RNA-RNA binding sites prediction
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Fast prediction of RNA-RNA interaction
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Time and space efficient RNA-RNA interaction prediction via sparse folding
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Hi-index | 3.84 |
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 incorporating accessibility of target sites as well as the existence of a user-definable seed. We successfully applied INTARNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs. Availability: http://www.bioinf.uni-freiburg.de/Software/ Contact: IntaRNA@informatik.uni-freiburg.de Supplementary information:Supplementary data are available at Bioinformatics online.