MOTIVATION Secondary structure prediction of RNA sequences is an important problem. There have been progresses in this area, but the accuracy of prediction from an RNA sequence is still limited. In many cases, however, homologous RNA sequences are available with the target RNA sequence whose secondary structure is to be predicted. RESULTS In this article, we propose a new method for secondary...

An RNA secondary structure is designable if there is an RNA sequence which can attain its maximum number of base pairs only by adopting that structure. The combinatorial RNA design problem, introduced by Haleš et al. in 2016, is to determine whether or not a given RNA secondary structure is designable. Haleš et al. identified certain classes of designable and non-designable secondary structures...

Pseudoknotted RNA secondary structure prediction is an important problem in computational biology. Existing polynomial time algorithms have no performance guarantee or can handle only limited types of pseudoknots. In this paper for the general problem of pseudoknotted RNA secondary structure prediction, a polynomial time approximation scheme is presented to predict pseudoknotted RNA secondary s...