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RNAmute specifications


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
GNU CC compiler
Maintained Yes


No version available


  • person_outline Danny Barash


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


  • person_outline Danny Barash

Publications for RNAmute

RNAmute citations


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

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. […]


Accurate Classification of RNA Structures Using Topological Fingerprints

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 […]


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

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 […]


Sampled ensemble neutrality as a feature to classify potential structured RNAs

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

[…] a sequence and those that differ by exactly one point mutation (1-mutant neighbors) []. There are a variety of existing computational methods [] and programs designed to evaluate RNA robustness (e.g. RNAmute, RDMAS, RSRE, RNAmutants, SNPfold, RNAsnp, RemuRNA, and Rchange) [,,-]. All of these approaches focus on a single input sequence and the ability of its neighboring mutants to maintain a “wild- […]


Detecting riboSNitches with RNA folding algorithms: a genome wide benchmark

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 […]


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

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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