Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming

Y. Kato, K. Sato, K. Asai, T. Akutsu
2012 Nucleic Acids Research  
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
doi:10.1093/nar/gks412 pmid:22600734 pmcid:PMC3394313 fatcat:yfg7rgc2zzee5a4b7aj42uj5qe