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Frnakenstein specifications

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Unique identifier OMICS_04758
Name Frnakenstein
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability No
Maintained No

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Publication for Frnakenstein

Frnakenstein citations

 (4)
library_books

Reconstruction of ancestral RNA sequences under multiple structural constraints

2016
BMC Genomics
PMCID: 5123390
DOI: 10.1186/s12864-016-3105-4

[…] 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 […]

library_books

RNAiFold2T: Constraint Programming design of thermo IRES switches

2016
Bioinformatics
PMCID: 4908349
PMID: 27307638
DOI: 10.1093/bioinformatics/btw265

[…] 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 […]

library_books

Multi objective optimization for RNA design with multiple target secondary structures

2015
BMC Bioinformatics
PMCID: 4559319
PMID: 26335276
DOI: 10.1186/s12859-015-0706-x

[…] 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 […]

library_books

Complete RNA inverse folding: computational design of functional hammerhead ribozymes

2014
Nucleic Acids Res
PMCID: 4191386
PMID: 25209235
DOI: 10.1093/nar/gku740

[…] 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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Frnakenstein institution(s)
Department of Statistics, University of Oxford, Oxford, UK

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