In this paper we model several simple biochemical operations on RNA molecules that modify their secondary structure by means of a suitable variation of Große-Rhode’s Algebra Transformation Systems.

Tree Adjunct Grammar for RNA (TAG 2 RNA ) is a new grammatical device to model RNA secondary structures including pseudoknots. An e cient parsing algorithm for this grammar is developed, and applied to some computational problems concerning RNA secondary structures. With this parser, we rst try to predict secondary structures of RNA sequences which are known to form pseudoknots structures, and ...

The spatial growth of small perturbations developing on a fully developed base flow in a duct with two inhomogeneous cross-flow directions is examined. For a laminar mean flow it is shown that optimally configured vortices at an upstream cross-section induce large transient amplification of a disturbance energy norm downstream. Such a linear growth is a likely initial stage of transition in duc...

The secondary structure for nucleic acids provides a level of description that is both abstract enough to allow for efficient algorithms and realistic enough to provide a good approximate to the thermodynamic and kinetics properties of RNA structure formation. The secondary structure model has furthermore been successful in explaining salient features of RNA evolution in nature and in the test ...

In the last ten years, several tools have been proposed for RNA secondary structure pairwise comparison. These tools use different models (ordered tree or forest, arc annotated sequence, multi-level tree) and methods (edit distance, alignment). We present a first online benchmark for comparing these tools. For various RNA families, we built two sets of secondary structures. The first, called th...

RNA secondary structures play a vital role in modern genetics and a lot of time and e ort has been put into their study. It is important to be able to predict them with high accuracy, since methods involving manual analysis are expensive, time-consuming and error-prone. Predictions can also be used to guide experiments to reduce time and money requirements. Several algorithms have been develope...

This paper proposes a grammatical tool, called tree adjunct grammar with tag for RNA ( denoted by TAG 2 RNA ), for representing secondary structures of RNAs, and shows some example TAG 2 RNA grammars for fairly complicated RNA secondary structures. We then demonstrate the appropriateness of the grammars for modeling RNA secondary structures by discussing its formal language and/or graph theoret...

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 7200-8500 nt. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an internal ribosomal entry site (IRES) region towards the 5'-end. T...

A bijective correspondence is established between secondary structures of a given rank and size and plane trees satisfying certain additional conditions. The correspondence is then used to obtain new combinatorial interpretations of Motzkin numbers in terms of plane trees and Dyck paths.

Compact polymers are self-avoiding random walks that visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform numerical calculations is generating a sufficiently large number of randomly sampled configurations. We present a Monte Carlo algorithm that uniformly samples com...