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MultiRNAFold specifications

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Unique identifier OMICS_15923
Name MultiRNAFold
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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  • person_outline Mirela Andronescu <>

Publication for MultiRNAFold

MultiRNAFold in publications

 (6)
PMCID: 4869172
PMID: 27173734
DOI: 10.1038/ncomms11538

[…] samples and the average rpm for each data set was used as measurement of expression. only regions with at least 20 reads in total were included in the analysis. free energy (δg) was determined by multirnafold., hek293 flp-in t-rex cells (invitrogen), hek293t and dicer ko hek293t cells (gifts from bryan cullen lab) were maintained under standard culture conditions. transfections were conducted […]

PMCID: 3731219
PMID: 23935479
DOI: 10.1371/journal.pcbi.1003172

[…] energy of formation, and δg ‡, the free energy of activation, by(9) , to compute the free energy and secondary structure of all species (single and complexes) of a system, we used the viennarna and multirnafold (when having more than two rna species) software. we only considered the minimum free energy state discarding the suboptimal ones. here, we did not consider pseudoknots. afterwards, […]

PMCID: 3347993
PMID: 22296803
DOI: 10.1186/1471-2105-13-22

[…] experiments, the most commonly used experimental approach to determine the free energy change of rna structures., we also consider variants of the turner model, used by andronescu et al. []. the t99-multirnafold (t99-mrf) model is derived from the turner99 model but includes only 363 features. parameters for features in the turner99 model can be obtained by extrapolation from the parameters […]

PMCID: 2881037
PMID: 20532037
DOI: 10.1371/journal.pone.0010961

[…] 17306 genomic hits, respectively. hits mapping to annotated regions (ucsc tables; rna genes and sno/mirna) were then eliminated (10561 and 8445, respectively) and rna secondary structure prediction (multirnafold version 1.1, ) were conducted on the remaining hits (11987 and 8861, respectively) including 70 nt of flanking genomic sequences. here, predicted rna structures having at least a 23 bp […]

PMCID: 2837027
PMID: 20181279
DOI: 10.1186/1471-2105-11-105

[…] each probe []. here we select four widely used, publicly available computer programs that implement the tnn model using large numbers of experimentally derived thermodynamic parameters, namely: the multirnafold v2.0 package [,] with two sets of thermodynamic parameters, the vienna package v1.8.1 [] and the unafold v3.5 package []., the multirnafold package (including the pairfold program […]


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MultiRNAFold institution(s)
Department of Computer Science, The University of British Columbia, Vancouver, BC, Canada
MultiRNAFold funding source(s)
This work was supported by supported by the National Science Foundation under grant numbers 0130108 and 0203892.

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