title: Abstract shape analysis of RNA.
abstract: Abstract shape analysis abstract shape analysis is a method to learn more about the complete Boltzmann ensemble of the secondary structures of a single RNA molecule. Abstract shapes classify competing secondary structures into classes that are defined by their arrangement of helices. It allows us to compute, in addition to the structure of minimal free energy, a set of structures that represents relevant and interesting structural alternatives. Furthermore, it allows to compute probabilities of all structures within a shape class. This allows to ensure that our representative subset covers the complete Boltzmann ensemble, except for a portion of negligible probability. This chapter explains the main functions of abstract shape analysis, as implemented in the tool RNA shapes. RNA shapes It reports on some other types of analysis that are based on the abstract shapes idea and shows how you can solve novel problems by creating your own shape abstractions.
authors.affiliation: Faculty of Technology and Center of Biotechnology, Bielefeld University, Bielefeld, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Janssen
authors.forename: Robert
authors.initials: R
authors.lastname: Giegerich
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D013816:Thermodynamics
chemical_list: D012313:RNA