A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures.

ABSTRACT:

Background

Improving accuracy and efficiency of computational methods that predict pseudoknotted RNA secondary structures is an ongoing challenge. Existing methods based on free energy minimization tend to be very slow and are limited in the types of pseudoknots that they can predict. Incorporating known structural information can improve prediction accuracy; however, there are not many methods for prediction of pseudoknotted structures that can incorporate structural information as input. There is even less understanding of the relative robustness of these methods with respect to partial information.

Results

We present a new method, Iterative HFold, for pseudoknotted RNA secondary structure prediction. Iterative HFold takes as input a pseudoknot-free structure, and produces

SUBMITTER: Jabbari H 

PROVIDER: S-EPMC4064103 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature