RNAplex: a fast tool for RNA-RNA interaction search.

@article{TAFER2008, abstract = {MOTIVATION: Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this mechanism. Additionally ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding putative target sites for newly discovered ncRNAs is a lengthy task as tools for cofolding RNA molecules like RNAcofold and RNAup are too slow for genome-wide search. Tools like RNAhybrid that neglects intramolecular interactions have runtimes proportional to \$\$\mathcal{O}\$\$ (m n), albeit with a large prefactor. Still in many cases the need for even faster methods exists. RESULTS: We present a new program, RNAplex, especially designed to quickly find possible hybridization sites for a query RNA in large RNA databases. RNAplex uses a slightly different energy model which reduces the computational time by a factor 10-27 compared to RNAhybrid. In addition a length penalty allows to focus the target search on short highly stable interactions. AVAILABILITY: RNAplex can be downloaded at http://www.tbi.univie.ac.at/\~{}htafer/ CONTACT: ivo@tbi.univie.ac.at.}, address = {Institute for Theoretical Chemistry, University of Vienna, W\"{a}hringerstrasse 17, A-1090 Vienna, Austria.}, author = {Tafer, Hakim and Hofacker, Ivo L L. }, citeulike-article-id = {2771735}, issn = {1460-2059}, journal = {Bioinformatics (Oxford, England)}, keywords = {interaction, rna-rna}, month = {April}, posted-at = {2008-05-08 15:08:57}, priority = {2}, title = {RNAplex: a fast tool for RNA-RNA interaction search.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/18434344}, year = {2008} }

TY - JOUR ID - TAFER2008 L3 - citeulike-article-id:2771735 TI - RNAplex: a fast tool for RNA-RNA interaction search. JF - Bioinformatics (Oxford, England) AD - Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria. SN - 1460-2059 N2 - MOTIVATION: Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this mechanism. Additionally ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding putative target sites for newly discovered ncRNAs is a lengthy task as tools for cofolding RNA molecules like RNAcofold and RNAup are too slow for genome-wide search. Tools like RNAhybrid that neglects intramolecular interactions have runtimes proportional to $$\mathcal{O}$$ (m n), albeit with a large prefactor. Still in many cases the need for even faster methods exists. RESULTS: We present a new program, RNAplex, especially designed to quickly find possible hybridization sites for a query RNA in large RNA databases. RNAplex uses a slightly different energy model which reduces the computational time by a factor 10-27 compared to RNAhybrid. In addition a length penalty allows to focus the target search on short highly stable interactions. AVAILABILITY: RNAplex can be downloaded at http://www.tbi.univie.ac.at/~htafer/ CONTACT: ivo@tbi.univie.ac.at. KW - interaction KW - rna-rna AU - Tafer, Hakim AU - Hofacker, Ivo L PY - 2008/04/23/ UR - http://view.ncbi.nlm.nih.gov/pubmed/18434344 ER -