title: Variations on RNA folding and alignment: lessons from Benasque.
abstract: Dynamic programming algorithms solve many standard problems of RNA bioinformatics in polynomial time. In this contribution we discuss a series of variations on these standard methods that implement refined biophysical models, such as a restriction of RNA folding to canonical structures, and an extension of structural alignments to an explicit scoring of stacking propensities. Furthermore, we demonstrate that a local structural alignment can be employed for ncRNA gene finding. In this context we discuss scanning variants for folding and alignment algorithms.
authors.affiliation: Zentralfriedhof Wien, 3. Tor Simmeringer Haupstrasse, Wien, Austria.
authors.forename: Athanasius F
authors.initials: AF
authors.lastname: Bompfünewerer
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.forename: Stephan H
authors.initials: SH
authors.lastname: Bernhart
authors.forename: Jana
authors.initials: J
authors.lastname: Hertel
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Sebastian
authors.initials: S
authors.lastname: Will
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D022661:RNA, Untranslated