We present a novel approach for detecting RNA shapes in given selected genes. Aside of the traditional sequencebased search methods such as BLAST and FASTA, there is a growing interest in detecting specific RNA secondary structure domains by using effective structure-based search methods such as the RNAMotif. Towards this end, we devise a new algorithm with ideas taken from computational geomet...

Stochastic Context-Free Grammars (SCFGs) have been used widely in modelling RNA secondary structure. They were motivated by the use of Hidden Markov Models (HMMs) in protein modelling (Krogh et al., (1993)). What was lacking in HMMs though, was the ability to model long range interactions which are necessary to provide an effective model for RNA secondary structure. Thus, SCFGs, as generalisati...

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 ...

The aim of the inverse folding problem for RNA is, given a target structure like e.g. the one depicted in Fig. 1, find a sequence that folds into this structure. In this project we will exclusively focus on the secondary structure. The main driving force behind RNA structure formation is the creation of base pairs similar to the ones observed in the DNA double helical structure. In RNA thymine ...

We present a novel approach for detecting RNA shapes in given selected genes. Aside of the traditional sequencebased search methods such as BLAST and FASTA, there is a growing interest in detecting specific RNA secondary structure domains by using effective structure-based search methods such as the RNAMotif. Towards this end, we devise a new algorithm with ideas taken from computational geomet...

RNA secondary structure consists of elements such as stems, bulges, loops. The most obvious and important scalar number that can be attached to an RNA structure is its free energy, with a landscape that governs the folding pathway. However, because of the unique geometry of RNA secondary structure, another interesting single-signed scalar number based on geometrical scales exists that can assis...