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Rfold specifications

Information


Unique identifier OMICS_15807
Name Rfold
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Source code URL https://www.ncrna.org/download/365/
Maintained Yes

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Maintainer


  • person_outline Hisanori Kiryu <>

Publication for Rfold

Rfold in publications

 (5)
PMCID: 5140013
PMID: 27980384
DOI: 10.4137/EBO.S40912

[…] states that 1/5 of the total mutations in every t iterations φ(t) should be successful mutations. according to the number of successes φ(t), the value of rf is adjusted according to rfnew(it+1)={rfold(t)*0.85ifφ(t)<1/5rfold(t)/0.85ifφ(t)>1/5rfold(t)ifφ(t)=1/5(13), the pseudocode is briefly described in ., de was first introduced by r. storn and k. v. price in 1995. in de […]

PMCID: 5045715
PMID: 27618451
DOI: 10.1038/ng.3664

[…] ‘phylop46way’ downloaded from the ucsc genome browser website was used to create the sequence conservation features. a basewise probability score for the mrna secondary structure was computed with rfold 0.1-2. optimal codon usage was used as a proxy for the translation efficiency and was computed by dividing the amount of optimal in-frame codons over the codon count. optimal codons […]

PMCID: 4109989
PMID: 25057821
DOI: 10.1371/journal.pone.0103041

[…] nt downstream of the mirna and the sequences 100 nt upstream and 20 nt downstream of the mirna were extracted to predict the rna secondary structure, and folded stem-loop structures were detected by rfold (http://www.tbi.univie.ac.at/~ivo/rna/rnafold.html) and analyzed by mireap (http://sourceforge.net/projects/mireap/) under the default settings. there are three characteristics in the structure […]

PMCID: 3496725
PMID: 23152777
DOI: 10.1371/journal.pone.0048485

[…] this study., the analysis of mirna expression in 13q-h and 13q-l cll patients revealed that fifteen mirnas were deregulated in 13q-h cll patients: hsa-mir-155 was the most highly upregulated mirna (rfold = 3.70), while hsa-mir-223 was the most significantly downregulated (rfold = 0.10). four of the deregulated mirnas (mir-15a, mir-29a, mir-155 and mir- 223) were further assayed by quantitative […]

PMCID: 3026369
PMID: 20946605
DOI: 10.1186/1471-2105-11-S6-S21

[…] the search for candidate rna motifs not yet discovered in nature or a laboratory., there are a number secondary rna structure prediction algorithms available online such as zuckers mfold and vienna rfold. given the primary rna sequence, the web server will return a list of predicted secondary folds. these programs are based on finding the secondary structure with the total lowest free energy […]


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Rfold institution(s)
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan; Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, Kashiwa, Chiba, Japan
Rfold funding source(s)
This work was partially supported by the ‘Functional RNA Project’ funded by the New Energy and Industrial Technology Development Organization (NEDO) of Japan.

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