RNAmute statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RNAmute
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Tool usage distribution map

This map represents all the scientific publications referring to RNAmute per scientific context
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Associated diseases

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Popular tool citations

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Protocols

RNAmute specifications

Information


Unique identifier OMICS_07476
Name RNAmute
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Java
Computer skills Advanced
Stability Stable
Requirements
GNU CC compiler
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Danny Barash

Information


Unique identifier OMICS_07476
Name RNAmute
Interface Web user interface
Restrictions to use None
Programming languages C, Java
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Danny Barash

Publications for RNAmute

RNAmute citations

 (10)
library_books

Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes

2017
Genome Biol
PMCID: 5343413
PMID: 28274275
DOI: 10.1186/s13059-017-1174-6

[…] predict whether DNMs causing synonymous change or locating at splicing sites (exon ±2 bp) created or disrupted splice sites []. To assess if synonymous DNMs had any effect on the transcripts, we used RNAmute []. Finally, ClinVar and PubMed were searched for the same or similar mutations in the same gene that present in healthy controls or other disease patients. […]

library_books

Accurate Classification of RNA Structures Using Topological Fingerprints

2016
PLoS One
PMCID: 5068708
PMID: 27755571
DOI: 10.1371/journal.pone.0164726

[…] to clustering and identifying biological RNAs with topologically similar structures. A coarse-grained RNA secondary structure representation has also been used to predict RNA deleterious mutations by RNAMute [] and RNAmutants []. In addition, a coarse-grained approach is also applied for RNA design such as RNAexinv [] and Nanofolder []. We demonstrate the utility of the XIOS approach by classifyin […]

library_books

The prediction of virus mutation using neural networks and rough set techniques

2016
EURASIP J Bioinform Syst Biol
PMCID: 4867776
PMID: 27257410
DOI: 10.1186/s13637-016-0042-0

[…] ity of the generation of any secondary structure is inversely proportional to the energy of this structure. This energy is modeled based on extensive thermodynamic measurements []. Applications like “RNAMute” analyzes the effects of point mutations on RNAs secondary structure based on thermodynamic parameters [].The third research direction is the prediction of single nucleotide variants (SNV) at […]

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

[…] rams designed to capture RNA structural robustness: bp-distance and PCC. First, bp-distance performance was evaluated using both the original method which only takes an input sequence, implemented in RNAmute, and a modified version we implemented, which requires a given sequence and structure. By comparing these bp-distance implementations, we examine the effect of the input structure on neutralit […]

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

[…] ance 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 between two RNA variants, predictions on dot bracket structur […]

library_books

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

2013
Hum Mutat
PMCID: 3708107
PMID: 23315997
DOI: 10.1002/humu.22273

[…] data there has been an increasing interest in computational tools to quantify the effects of SNPs in more detail. Several tools use graph-theoretical descriptors to evaluate the effect, for example, RNAmute [Barash, ; Churkin and Barash, ] and RDMAS [Shu et al., ]. SNPfold [Halvorsen et al., ] uses the Pearson correlation of pairing probabilities of wild-type and mutant to quantify the structural […]


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RNAmute institution(s)
Department of Computer Science, Ben-Gurion University, Beer Sheva, Israel

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