title: Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.
abstract: Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary information with traditional energy-based RNA folding algorithms. Here we describe the theory and applications of the RNAalifold algorithm. Consensus secondary structure prediction not only leads to significantly more accurate structure models, but it also allows to study structural conservation of functional RNAs.
authors.affiliation: Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
authors.forename: Stefan
authors.initials: S
authors.lastname: Washietl
authors.forename: Stephan H
authors.initials: SH
authors.lastname: Bernhart
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016384:Consensus Sequence; D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D013816:Thermodynamics; D064878:Web Browser
chemical_list: D012313:RNA