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Publication for Frnakenstein
Reconstruction of ancestral RNA sequences under multiple structural constraints
[…] with RNAdistance  between the structures 0 and 1, 0 and 2, and 1 and 2 are respectively 40, 96 and 86.For every pair of secondary structures, a set of twenty bi-stable sequences was generated with Frnakenstein , such that the best scoring sequence of each run was kept. For each pair of structures (s 1,s 2), and each sequence z designed on these structures, a complete binary tree T of depth 6 […]
RNAiFold2T: Constraint Programming design of thermo IRES switches
[…] SwitchDesign (SD) (), Frnakenstein (FRNA) (), and RNAiFold2T were benchmarked on Rfam family RF01804 of Lambda phage CIII thermoregulator elements to determine the maximum number of distinct solutions over 24 h, restarting […]
Multi objective optimization for RNA design with multiple target secondary structures
[…] NA and RNAdesign are statistically significant (< 0.05 /4). Since we tested four comparisons (a comparison between δ e 1s of MODENA and RNAdesign, δ e 2s of MODENA and RNAdesign, δ e 1s of MODENA and Frnakenstein, and δ e 2s of MODENA and Frnakenstein),“0.05 divided by four” was used here as the level of statistical significance for each comparison.At the bottom of Table , the means and medians fo […]
Complete RNA inverse folding: computational design of functional hammerhead ribozymes
[…] ndary structures (); nevertheless, a number of heuristic algorithms exist that return approximate solutions: RNAinverse (), switch.pl (), RNA-SSD (), INFO-RNA (), MODENA (), NUPACK-DESIGN (), Inv (), Frnakenstein (). Rather than employing a heuristic, our recent software, RNAiFold (,), employs Constraint Programming (CP) (), which always returns exact solutions, although it might do so in an impra […]
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