RNA structure is crucial for gene regulation and function. In the past, transcriptomes have
largely been parsed by primary sequences and expression levels, but it is now becoming …

RNA secondary structure is often predicted from sequence by free energy minimization.
Over the past two years, advances have been made in the estimation of folding free energy …

Motivation: For several decades, free energy minimization methods have been the dominant
strategy for single sequence RNA secondary structure prediction. More recently, stochastic …

Motivation: Pseudoknots found in secondary structures of a number of functional RNAs play
various roles in biological processes. Recent methods for predicting RNA secondary …

A partition function calculation for RNA secondary structure is presented that uses a current
set of nearest neighbor parameters for conformational free energy at 37° C, including …

Prediction of RNA secondary structure by free energy minimization has been the standard
for over two decades. Here we describe a novel method that forsakes this paradigm for …

Secondary structure plays an important role in determining the function of noncoding RNAs.
Hence, identifying RNA secondary structures is of great value to research. Computational …

Background An increasing number of researchers have released novel RNA structure
analysis and prediction algorithms for comparative approaches to structure prediction. Yet …

The Kinefold web server provides a web interface for stochastic folding simulations of
nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional …

We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary
structures including pseudoknots. Based on the simple idea of iteratively forming stable …