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RDMAS specifications

Information


Unique identifier OMICS_07480
Name RDMAS
Interface Web user interface
Restrictions to use None
Programming languages C, PHP
License GNU General Public License version 2.0
Computer skills Basic
Stability No
Requirements
Vienna RNA
Maintained No

Maintainer


This tool is not available anymore.

Publication for RDMAS

RDMAS citations

 (6)
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

[…] e 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-type” str […]

library_books

A Novel Artificial Immune Algorithm for Spatial Clustering with Obstacle Constraint and Its Applications

2014
Comput Intell Neurosci
PMCID: 4236973
PMID: 25435862
DOI: 10.1155/2014/160730

[…] o (). For all ab i, ab i ∈ M, if the value of f i,j′ is less than α, randomly delete one of the two antibodies.Randomly generate antibody subset to update the next generation antibody set, denoted by rdmAS.Add M and rdmAS to Abs(t + 1). Consider t = t + 1. Obtain bstAS1 via performing clone operation on bstAS.Obtain bstAS2 via performing mutation operation on bstAS1. Add bstAS2 to M.Implement the […]

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

[…] n 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 effect of the SNP and to identify “RiboSNitc […]

library_books

Multi scale RNA comparison based on RNA triple vector curve representation

2012
BMC Bioinformatics
PMCID: 3599440
PMID: 23110635
DOI: 10.1186/1471-2105-13-280

[…] it is very important to search the most significant point mutation. Our proposed method is very efficient to find the significant point mutation compared with the popular RNA mutation analysis tool: RDMAS []. RDMAS is a web server for evaluating structural deleteriousness of single nucleotide mutation in RNA genes. We evaluate single nucleotide structure mutation microRNA miR-21 precursor based o […]

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

[…] kes 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 in the mutation prediction problem [], mainly in the generalization to multiple-point mutations that can become computationally heavy i […]

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

[…] mational rearranging point mutation by traversing all possible single point mutations of a sequence and locate the most significant ones, in terms of secondary structure difference []. RNAMute [] and RDMAS [] are tools that attempt to perform such predictions and are based on energy minimization methods [,]. The RNAMute mutation analysis tool, [], includes RNAdistance from [,]: the RNA edit distan […]

Citations

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RDMAS institution(s)
Beijing Institute of Radiation Medicine, Beijing, China

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