A workshop entitled ''Computational approaches to noncoding RNAs'' will be held in Benasque (Spain) from the 16th of July to the 28th of July 2006. We expect to gather a group of (approximately 55) mostly theoreticians and computational scientists working on problems related to the computational analysis of functional and regulatory RNAs. The major objective is to present and discuss the state of RNA computational biology, to identify the needs, and to propose new developments for the identification, annotation, and the computational analysis of functional and regulatory RNAs present in genomes. Besides and beyond transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), new RNAs such as micro RNAs, riboswitches, or regulatory RNAs in bacteria (broadly called noncoding RNAs or ncRNAs) have become extremely active areas of research in basic science like cell development and fate but also in cancer and therapeutic research. Specifically, some of the issues that will be discussed are: (1) RNA structure prediction, Structural alignments, RNA homology search; (2) RNA genefinding and genome annotation; (3) RNA databases and RNA Ontology. The ncRNA genefinding and the reliable annotation of Eukaryotic genomes is a very important tasks for computational biologists working on RNA. The extension to multiple sequences is an important advance for ncRNA genefinders, and new screens in higher organisms are likely to appear in the near future. As in the case of folding algorithms there is also a dichotomy between thermodynamic-based algorithms and methods based on pair stochastic context-free grammars that need to be clarified. Additionally improved grammatical models to describe RNAs, better training of the parameters of the models, and more complex objective functions to describe the nature of a functional RNA will be discussed.
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