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Publication for remuRNA
Functional and Structural Consequence of Rare Exonic Single Nucleotide Polymorphisms: One Story, Two Tales
[…] 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 […]
The potential of the riboSNitch in personalized medicine
[…] 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 […]
Sampled ensemble neutrality as a feature to classify potential structured RNAs
[…] 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 […]
Detecting riboSNitches with RNA folding algorithms: a genome wide benchmark
[…] 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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