title: Fast alignment and comparison of RNA structures.
abstract: BACKGROUND
  To recognize remote relationships between RNA molecules, one must be able to align structures without regard to sequence similarity. We have implemented a method, which is swift [O(n(2))], sensitive and tolerant of large gaps and insertions. Molecules are broken into overlapping fragments, which are characterized by their memberships in a probabilistic classification based on local geometry and H-bonding descriptors. This leads to a probabilistic similarity measure that is used in a conventional dynamic programming method.
  
  
  RESULTS
  Examples are given of database searching, the detection of structural similarities, which would not be found using sequence based methods, and comparisons with a previously published approach.
  
  
  METHODS
  Source code (C and perl) and binaries for linux are freely available at www.zbh.uni-hamburg.de/fries.
authors: Centre for Bioinformatics, University of Hamburg, Bundesstr. 43, D-20146 Hamburg, Germany. tim.wiegels@gmail.com
authors: Tim
authors: T
authors: Wiegels
authors: Stefan
authors: S
authors: Bienert
authors: Andrew E
authors: AE
authors: Torda
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D012313:RNA