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RNAmutants specifications

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Unique identifier OMICS_07479
Name RNAmutants
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for RNAmutants

RNAmutants citations

 (7)
library_books

Accurate Classification of RNA Structures Using Topological Fingerprints

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

[…] nd 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 classifying a representat […]

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

[…] structures generated for mutant sequences using the Vienna RNA package [,,]. However, using the MFE structure as the sole reference limits the accuracy of predicted structure disrupting mutations []. RNAmutants samples mutant sequences and structures according to their probability in the structural ensemble to identify sequences that severely disrupt structure, but fundamentally determines the str […]

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

[…] uctures are referred to as MFE structures in this benchmark. CentroidFold, CONTRAfold, RNAfold (), RNAstruture () and UNAFold () are capable of returning both MFE structures and BPPMs. MC-Fold () and RNAmutants () return only MFE structures. MFE structures were compared with the RNAdistance function from ViennaRNA 2.1.1 and BPPMs were compared with RNApdist. The RNApdist function used here is a mo […]

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

[…] ral effect of the SNP and to identify “RiboSNitches,” that is, SNPs with particularly dramatic effects on the RNA structure. The corRna web server [Lam et al., ] adheres to the same strategy but uses RNAmutants [Waldispühl et al., ] to compute the structural ensembles for the entire k-neighborhood of the reference sequence. Rchange [Kiryu and Asai, ], differs from the above approaches as it does n […]

library_books

Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches

2012
PLoS One
PMCID: 3526635
PMID: 23284639
DOI: 10.1371/journal.pone.0050506

[…] present we see how to use FFTbor to sample structures from the Boltzmann ensemble of structures having base pair distance from .In , , we introduced the a related parametric RNA structure algorithm, RNAmutants, which computes the partition function and minimum free energy structure over all secondary structures of all -point mutants of a given RNA sequence . In , RNAmutants was extended to samp […]

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

[…] In general, neither the original RNAMute [] nor RDMAS [] can handle multiple-point mutations. Consequently, RNAMute [] was extended to MultiRNAMute [] and based on the approach of [], the web servers RNAmutants [] and later corRna [] were developed. A web server for MultiRNAMute was worked out in []. There is, however, one common feature that should be taken into account when considering all of th […]


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RNAmutants institution(s)
Department of Mathematics, MIT, Cambridge, MA, USA

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