RNAcop (RNA Context Optimization by Probability) is a tool to optimize lengths of flanking regions up- and downstream of a probable structure fold. The RNAcop algorithm progressively adds nucleotides to flanking regions of a sequence to determine the one having the highest probability of a constrained structure.
RNA; Bioinformatics; Nucleic acid structure analysis
Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J "Optimizing RNA structures by sequence extensions using RNAcop." Nucleic Acids Res. 2015; 43(17):8135-45 https://doi.org/10.1093/nar/gkv813
PMID: 26283181
PMCID: PMC4787817
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