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Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets of non-coding small RNAs that regulate gene expression post-transcriptionally. A number of computational studies have so far been devoted to predicting joint secondary structures or binding sites under a specific class of interactions.
(Kato et al., 2010) RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics.