title: Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.
abstract: We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational tools based on integer programming, IPknot for predicting RNA secondary structures with pseudoknots and RactIP for predicting RNA-RNA interactions with kissing hairpins. Both servers can run much faster than existing services with the same purpose on large data sets as well as being at least comparable in prediction accuracy. The Rtips web server along with the stand-alone programs is freely accessible at http://rna.naist.jp/.
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. ykato@is.naist.jp
authors.forename: Yuki
authors.initials: Y
authors.lastname: Kato
authors.forename: Kengo
authors.initials: K
authors.lastname: Sato
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Akutsu
mesh_terms: D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA