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RDMAS specifications


Unique identifier OMICS_07480
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
Vienna RNA
Maintained No


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Publication for RDMAS

RDMAS citations


Sampled ensemble neutrality as a feature to classify potential structured RNAs

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 […]


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

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 […]


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

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 […]


Multi scale RNA comparison based on RNA triple vector curve representation

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 […]


Efficient procedures for the numerical simulation of mid size RNA kinetics

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 […]


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

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 […]


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

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