title: Prediction of consensus RNA secondary structures including pseudoknots.
abstract: Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here, we present a method for computing the consensus structures including pseudoknots based on alignments of a few sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm. We applied our algorithm to a number of different types of RNA known to contain pseudoknots. All pseudoknots were predicted correctly and more than 85 percent of the base pairs were identified.
authors.affiliation: Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Wahringerstrasse 17, A-1090 Wien, Austria. xtina@tbi.univie.ac.at
authors.forename: Christina
authors.initials: C
authors.lastname: Witwer
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012329:RNA, Bacterial / Q000737:chemistry; D016415:Sequence Alignment / Q000706:statistics & numerical data; D013816:Thermodynamics
chemical_list: D012329:RNA, Bacterial; D012313:RNA