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

We present a web-based tool set for fast and accurate prediction of RNA 2D complex structures. comprises two computational tools based on integer programming, for predicting RNA secondary structures with pseudoknots and 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 web server along with the stand-alone programs is freely accessible at http://rna.naist.jp/..