title: RNAshapes: an integrated RNA analysis package based on abstract shapes.
abstract: We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach.
authors.affiliation: Faculty of Technology and, Bielefeld University, 33594 Bielefeld, Germany. psteffen@techfak.uni-bielefeld.de
authors.forename: Peter
authors.initials: P
authors.lastname: Steffen
authors.forename: Björn
authors.initials: B
authors.lastname: Voss
authors.forename: Marc
authors.initials: M
authors.lastname: Rehmsmeier
authors.forename: Jens
authors.initials: J
authors.lastname: Reeder
authors.forename: Robert
authors.initials: R
authors.lastname: Giegerich
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010363:Pattern Recognition, Automated / Q000379:methods; D012313:RNA / Q000032:analysis / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D012313:RNA