RactIP provides services for predicting RNA joint secondary structures under the general type of interaction including kissing hairpins. RactIP runs fast and predicts the maximum expected accuracy (MEA) structure using integer programming (IP) with threshold cut. RactIP can integrate approximate information on an ensemble of equilibrium joint structures into the objective function of integer programming using posterior internal and external base-paring probabilities.
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Y. Kato, K. Sato, K. Asai and T. Akutsu,
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming,
Nucleic Acids Res., 40, W29-W34, 2012
Y. Kato, K. Sato, M. Hamada, Y. Watanabe, K. Asai and T. Akutsu,
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming,
Bioinformatics, vol. 26, no. 18, pp. i460-i466, 2010.