Background The general problem of RNA secondary structure prediction under the widely
used thermodynamic model is known to be NP-complete when the structures considered …

In this review paper we discuss fatgraphs as a conceptual framework for RNA structures. We
discuss various notions of coarse-grained RNA structures and relate them to fatgraphs. We …

Motivation: Several dynamic programming algorithms for predicting RNA structures with
pseudoknots have been proposed that differ dramatically from one another in the classes of …

Motivation: RNA structure motifs contained in mRNAs have been found to play important
roles in regulating gene expression. However, identification of novel RNA regulatory motifs …

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 …

Computational methods for predicting evolutionarily conserved rather than thermodynamic
RNA structures have recently attracted increased interest. These methods are indispensable …

Bioinformatics is an active research area aimed at develo** intelligent systems for
analyses of molecular biology. Many methods based on formal language theory, statistical …

The view of RNA as simple information transfer molecule has been continuously challenged
since the discovery of ribozymes, a class of RNA molecules with enzyme-like function …

Motivation RNA H-type pseudoknots are ubiquitous pseudoknots that are found in almost all
classes of RNA and thought to play very important roles in a variety of biological processes …

The most probable secondary structure of an RNA molecule, given the nucleotide sequence,
can be computed efficiently if a stochastic context-free grammar (SCFG) is used as the prior …