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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

 (7)
library_books

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

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

[…] 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., evidence of gene-level […]

library_books

Accurate Classification of RNA Structures Using Topological Fingerprints

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

[…] 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 […]

library_books

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

2016
PMCID: 4867776
PMID: 27257410
DOI: 10.1186/s13637-016-0042-0

[…] 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) […]

library_books

Sampled ensemble neutrality as a feature to classify potential structured RNAs

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

[…] 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 […]

library_books

Efficient procedures for the numerical simulation of mid size RNA kinetics

2012
PMCID: 3463434
PMID: 22958879
DOI: 10.1186/1748-7188-7-24

[…] [,] and have been substantially revived in [,]. the first publicly available program for the rna mutation prediction problem that takes into account only single-point mutation predictions was called rnamute [,]. it uses the vienna rna package in its core. subsequently, a web server dealing with similar issues was put forth called rdmas []. there are also some computationally challenging issues […]

library_books

An image processing approach to computing distances between RNA secondary structures dot plots

2009
PMCID: 2677394
PMID: 19203377
DOI: 10.1186/1748-7188-4-4

[…] using the lempel-ziv algorithm was suggested in []. another method uses the second eigenvalue of the tree graph representation for the structures comparison, [], and was later integrated into the rnamute [], a java tool, which we will use for our second application illustration. the latter aforementioned method is not a metric. a comparison on metric methods is available in [], […]


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

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