KnotSeeker: Heuristic pseudoknot detection in long RNA sequences

@article{citeulike:2575068, abstract = {Pseudoknots are folded structures in RNA molecules that perform essential functions as part of cellular transcription machinery and regulatory processes. The prediction of these structures in RNA molecules has important implications in antiviral drug design. It has been shown that the prediction of pseudoknots is an NP-complete problem. Practical structure prediction algorithms based on free energy minimization employ a restricted problem class and dynamic programming. However, these algorithms are computationally very expensive, and their accuracy deteriorates if the input sequence containing the pseudoknot is too long. Heuristic methods can be more efficient, but do not guarantee an optimal solution in regards to the minimum free energy model. We present KnotSeeker, a new heuristic algorithm for the detection of pseudoknots in RNA sequences as a preliminary step for structure prediction. Our method uses a hybrid sequence matching and free energy minimization approach to perform a screening of the primary sequence. We select short sequence fragments as possible candidates that may contain pseudoknots and verify them by using an existing dynamic programming algorithm and a minimum weight independent set calculation. KnotSeeker is significantly more accurate in detecting pseudoknots compared to other common methods as reported in the literature. It is very efficient and therefore a practical tool, especially for long sequences. The algorithm has been implemented in Python and it also uses C/C++ code from several other known techniques. The code is available from http://www.csse.uwa.edu.au/[~]datta/pseudoknot. 10.1261/rna.968808}, author = {Sperschneider, Jana and Datta, Amitava }, citeulike-article-id = {2575068}, doi = {10.1261/rna.968808}, journal = {RNA}, keywords = {pseudoknots}, month = {April}, number = {4}, pages = {630--640}, posted-at = {2008-03-26 20:41:57}, priority = {2}, title = {KnotSeeker: Heuristic pseudoknot detection in long RNA sequences}, url = {http://dx.doi.org/10.1261/rna.968808}, volume = {14}, year = {2008} }

TY - JOUR ID - citeulike:2575068 L3 - citeulike-article-id:2575068 TI - KnotSeeker: Heuristic pseudoknot detection in long RNA sequences JF - RNA VL - 14 IS - 4 SP - 630 EP - 640 N2 - Pseudoknots are folded structures in RNA molecules that perform essential functions as part of cellular transcription machinery and regulatory processes. The prediction of these structures in RNA molecules has important implications in antiviral drug design. It has been shown that the prediction of pseudoknots is an NP-complete problem. Practical structure prediction algorithms based on free energy minimization employ a restricted problem class and dynamic programming. However, these algorithms are computationally very expensive, and their accuracy deteriorates if the input sequence containing the pseudoknot is too long. Heuristic methods can be more efficient, but do not guarantee an optimal solution in regards to the minimum free energy model. We present KnotSeeker, a new heuristic algorithm for the detection of pseudoknots in RNA sequences as a preliminary step for structure prediction. Our method uses a hybrid sequence matching and free energy minimization approach to perform a screening of the primary sequence. We select short sequence fragments as possible candidates that may contain pseudoknots and verify them by using an existing dynamic programming algorithm and a minimum weight independent set calculation. KnotSeeker is significantly more accurate in detecting pseudoknots compared to other common methods as reported in the literature. It is very efficient and therefore a practical tool, especially for long sequences. The algorithm has been implemented in Python and it also uses C/C++ code from several other known techniques. The code is available from http://www.csse.uwa.edu.au/[~]datta/pseudoknot. 10.1261/rna.968808 KW - pseudoknots AU - Sperschneider, Jana AU - Datta, Amitava PY - 2008/04/01/ UR - http://dx.doi.org/10.1261/rna.968808 ER -