Covariance models are a powerful description of non-coding RNA (ncRNA) families that can be used to search nucleotide databases for new members of these ncRNA families. Currently, estimation of the parameters of a covariance model (state transition and emission scores) is based only on the...

A suitable model to dive into the properties of genotype-phenotype landscapes is the relationship between RNA sequences and their corresponding minimum free energy secondary structures. Relevant issues related to molecular evolvability and robustness to mutations have been studied in this...

The family Picornaviridae contains important pathogens including, for example, Hepatitis A virus and Foot-and-Mouth Disease Virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200 to 8500nts. Besides coding for the viral proteins, it also contains functionally important...

Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with...

We show that the problem of designing RNA sequences that can fold into multiple stable secondary structures can be transformed into a combinatorial optimization problem that can be solved by means of simple heuristics. Hence it is feasible to design RNA switches with prescribed strucutral...

We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss folding mechanisms and the correlation between the barrier structure of the conformational...

RNA folding from sequences into secondary structures is a simple yet powerful, biophysically grounded model of a genotype-phenotype map in which concepts like plasticity, evolvability, epistasis and modularity not only can be precisely defined and statistically measured, but reveal simultaneous...

To distinguish continuous from discontinuous evolutionary change, a relation of nearness between phenotypes is needed. Such a relation is based on the probability of one phenotype being accessible from another through changes in the genotype. This is exemplified by calculating the shape...

An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm performs particularly well in the vicinity of the minimum free energy. This enables the efficient approximation of statistical...

Folding of RNA sequences into secondary structures is viewed as a map that assigns a uniquely defined base pairing pattern to every sequence. This mapping is non-invertible since many sequences fold into the same (secondary) structure or shape. The preimages of the map, called neutral networks,...