RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound
نویسندگان
چکیده
Predicting the secondary structure of an RNA sequence is an important problem in structural bioinformatics. The general RNA folding problem, where the sequence to be folded may contain pseudoknots, is computationally intractable when no prior knowledge on the pseudoknot structures the sequence contains is available. In this paper, we consider stable stems in an RNA sequence and provide a new characterization for its stem graph, a graph theoretic model that has been used to describe the overlapping relationships for stable stems. Based on this characterization, we identify a new structure parameter for a stem graph. We call this structure parameter crossing width. We show that given a sequence with crossing width c for its stem graph, the general RNA folding problem can be solved in time O(2kn), where n is the length of the sequence, k is the maximum length of stable stems. Moreover, this characterization leads to an O(2 2)nn2k3) time algorithm for the general RNA folding problem where the lengths of stems in the sequence are at most k, this result improves the upper bound of the problem to 2n when the maximum stem length is bounded by a constant.
منابع مشابه
Characteristics and Prediction of RNA Structure
RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is NP-hard. Most RNAs fold during transcription from DNA into RNA through a hierarchical pathway wherein secondary structures form prior to tertiary structures. Real RNA secondary structures often have local instead of global optimization because of kinetic reasons. The performance of RNA structure pr...
متن کامل91 17 v 1 2 9 Se p 20 03 Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on...
متن کاملPrediction of RNA pseudoknots by Monte Carlo simulations
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the non-planar topologies of RNA structures and propose a classification of RNA pseudoknots according to the minimal genus of the surface on which the RNA structu...
متن کاملPrediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here we report that many pseudoknots can be predicted through long-time-scale RNA-folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on a...
متن کاملpknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
RNA pseudoknots are an important structural feature of RNAs, but often neglected in computer predictions for reasons of efficiency. Here, we present the pknotsRG Web Server for single sequence RNA secondary structure prediction including pseudoknots. pknotsRG employs the newest Turner energy rules for finding the structure of minimal free energy. The algorithm has been improved in several ways ...
متن کامل