RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0, i.e. whose minimum free energy secondary structure is identical to the targetâ€¦ (More)

Vienna RNA Package software Kinfold implements the Gillespie algorithm for RNA secondary structure folding kinetics, for the move sets MS1 [resp. MS2], consisting of base pair additions and removalsâ€¦ (More)

We describe the first dynamic programming algorithm that computes the expected degree for the network, or graph G = (V, E) of all secondary structures of a given RNA sequence a = a1, â€¦, an. Here, theâ€¦ (More)

Background: Existent programs for RNA folding kinetics, such as Kinefold, Kinfold and KFOLD,<lb>implement the Gillespie algorithm to generate stochastic folding trajectories from an initial structureâ€¦ (More)

RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exactâ€¦ (More)

RNA molecules can be designed by applying an optimization method (adaptive walk, Monte-Carlo, genetic algorithm, constraint programming, etc) to compute sequences that are likely to fold into a givenâ€¦ (More)

Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstreamâ€¦ (More)