RNAcop (RNA Context Optimization by Probability) is a tool for optimizing lengths of flanking regions up- and downstream of a constrained structure with respect to the probability of folding into the structure.
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Optimizing RNA structures by sequence extensions using RNAcop.
Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J.
Nucleic Acids Res. 2015 Sep 30;43(17):8135-45. doi: 10.1093/nar/gkv813.