DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model.

ABSTRACT: RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accuracy for longer sequences. A heuristic approach is to search for promising pseudoknot candidates in a sequence and verify those. Afterwards, the detected pseudoknots can be further analysed using bioinformatics or laboratory techniques. We present a novel pseudoknot detection method called DotKnot that extracts stem regions from the secondary structure probability dot plot and assembles pseudoknot candidates in a constructive fashion. We evaluate pseudoknot free energies using n

SUBMITTER: Sperschneider J 

PROVIDER: S-EPMC2853144 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature