HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots Export

@article{hotknots, abstract = {10.1261/rna.7284905 We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems. In an empirical evaluation of the algorithm with 43 sequences taken from the Pseudobase database and from the literature on pseudoknotted structures, we found that overall, in terms of the sensitivity and specificity of predictions, HotKnots outperforms the well-known Pseudoknots algorithm of Rivas and Eddy and the NUPACK algorithm of Dirks and Pierce, both based on dynamic programming approaches for limited classes of pseudoknotted structures. It also outperforms the heuristic Iterated Loop Matching algorithm of Ruan and colleagues, and in many cases gives better results than the genetic algorithm from the STAR package of van Batenburg and colleagues and the recent pknotsRG-mfe algorithm of Reeder and Giegerich. The HotKnots algorithm has been implemented in C/C++ and is available from .}, address = {Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.}, author = {Ren, Jihong and Rastegari, Baharak and Condon, A. N. N. E. and Hoos, Holger H.}, citeulike-article-id = {494445}, citeulike-linkout-0 = {http://dx.doi.org/10.1261/rna.7284905}, citeulike-linkout-1 = {http://rnajournal.cshlp.org/content/11/10/1494.abstract}, citeulike-linkout-2 = {http://rnajournal.cshlp.org/content/11/10/1494.full.pdf}, citeulike-linkout-3 = {http://www.rnajournal.org/cgi/content/abstract/11/10/1494}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/16199760}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=16199760}, doi = {10.1261/rna.7284905}, issn = {1355-8382}, journal = {RNA}, keywords = {folding, heuristic, hotknots, rna, thesis}, month = {October}, number = {10}, pages = {1494--1504}, posted-at = {2008-03-26 18:07:56}, priority = {2}, title = {HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots}, url = {http://dx.doi.org/10.1261/rna.7284905}, volume = {11}, year = {2005} }

TY - JOUR ID - hotknots L3 - citeulike-article-id:494445 N2 - 10.1261/rna.7284905 We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems. In an empirical evaluation of the algorithm with 43 sequences taken from the Pseudobase database and from the literature on pseudoknotted structures, we found that overall, in terms of the sensitivity and specificity of predictions, HotKnots outperforms the well-known Pseudoknots algorithm of Rivas and Eddy and the NUPACK algorithm of Dirks and Pierce, both based on dynamic programming approaches for limited classes of pseudoknotted structures. It also outperforms the heuristic Iterated Loop Matching algorithm of Ruan and colleagues, and in many cases gives better results than the genetic algorithm from the STAR package of van Batenburg and colleagues and the recent pknotsRG-mfe algorithm of Reeder and Giegerich. The HotKnots algorithm has been implemented in C/C++ and is available from . IS - 10 JF - RNA SN - 1355-8382 AD - Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. EP - 1504 TI - HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots VL - 11 SP - 1494 KW - folding KW - heuristic KW - hotknots KW - rna KW - thesis AU - Ren, Jihong AU - Rastegari, Baharak AU - Condon, ANNE AU - Hoos, Holger PY - 2005/10// UR - http://dx.doi.org/10.1261/rna.7284905 ER -