remuRNA statistics

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remuRNA specifications

Information


Unique identifier OMICS_07475
Name remuRNA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for remuRNA

remuRNA citations

 (4)
library_books

Functional and Structural Consequence of Rare Exonic Single Nucleotide Polymorphisms: One Story, Two Tales

2015
Genome Biol Evol
PMCID: 4684694
PMID: 26454016
DOI: 10.1093/gbe/evv191

[…] y change mRNA structure is widespread (; ; , , , ; ). Here, we examined the relationship between DAF of exonic SNPs and corresponding alteration in mRNA secondary structure. Two independent programs, remuRNA () and RNAsnp (), were used to predict the effect of single-point mutation on local mRNA secondary structure. remuRNA computes the structural entropy in Boltzmann ensembles between wild-type a […]

library_books

The potential of the riboSNitch in personalized medicine

2015
PMCID: 4543445
PMID: 26115028
DOI: 10.1002/wrna.1291

[…] re not ideal for predicting SNV‐induced changes to the structural ensemble. Several algorithms have been developed to predict the impact of SNPs on structural ensembles including SNPfold, RNAsnp, and remuRNA., , In this approach, the full Boltzmann weighted suboptimal structural ensemble is computed for each sequence variant and the base‐pairing probabilities per nucleotide calculated. This enabl […]

library_books

Sampled ensemble neutrality as a feature to classify potential structured RNAs

2015
BMC Genomics
PMCID: 4333902
PMID: 25649229
DOI: 10.1186/s12864-014-1203-8

[…] that of its mutants using the Pearson’s correlation coefficient (PCC) [], and RNAsnp uses this measure in combination with the base-pair distance to evaluate structural similarity and disruption []. RemuRNA measures the effect of a mutation on the entire RNA secondary structure distribution using relative entropy rather than sampling from the structural ensemble []. Alternatively, Rchange takes a […]

call_split

Detecting riboSNitches with RNA folding algorithms: a genome wide benchmark

2015
Nucleic Acids Res
PMCID: 4330374
PMID: 25618847
DOI: 10.1093/nar/gkv010
call_split See protocol

[…] Table S4. The ‘specialized’ algorithms directly score the distance between sequence pairs. SNPfold () scores with a Pearson correlation coefficient, RNAsnp () returns a P-value on Euclidean distance, remuRNA () measures the relative entropy between two RNAs and RNAmute () measures the edit distance between MFE structures. For algorithms that do not intrinsically compare the structures of sequences […]

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remuRNA institution(s)
National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA

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