RNA Sampler statistics

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RNA Sampler specifications

Information


Unique identifier OMICS_03480
Name RNA Sampler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for RNA Sampler

RNA Sampler in publications

 (5)
PMCID: 4339682
PMID: 25727492
DOI: 10.1186/s12859-015-0464-9

[…] with aligning a pseudoknot structure with a sequence or genome. through the alignment, the sequence is folded and its structure is predicted. xu et al. [] presented a different method, called rna sampler, which can simultaneously fold and align two or multiple rna sequences considering pseudoknots without known structures. similar techniques were implemented in dafs [] and simulfold []. […]

PMCID: 2709569
PMID: 19429694
DOI: 10.1093/nar/gkp276

[…] sampling methodology, on the other hand, extensions of the technique to multiple sequences have received limited attention. although a heuristic iterative sampling methodology has been proposed in rna sampler (), a true stochastic sampling framework has not been previously developed due to the difficulty in computing the corresponding partition function for the multiple homolog scenario., […]

PMCID: 2659441
PMID: 19343219
DOI: 10.1371/journal.pcbi.1000338

[…] identification of novel regulatory rnas are strongly desired to facilitate our exploration of gene regulation mechanisms and regulatory networks. we present a new computational program named rssvm (rna sampler+support vector machine), which employs support vector machines (svms) for efficient identification of functional rna motifs from random rna secondary structures. rssvm uses a set […]

PMCID: 2387179
PMID: 18439255
DOI: 10.1186/1471-2105-9-212

[…] score (sps) criterion. as a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as rna sampler. the x-ins-i framework can be used for building a multiple rna alignment from any combination of algorithms for pairwise rna alignment and base-pairing probability. the source code […]

PMCID: 4292096
DOI: 10.1186/1471-2105-8-S8-P8

[…] for rna sequences was described by sankoff [], but to date only pairwise implementations (e.g. foldalign [], dynalign []) or heuristics for multiple sequences (e.g. foldalignm [], locarna [], rna sampler []) exist., we present a novel approach to the problem: using markov chain monte carlo in a simulated annealing framework, we sample multiple alignments and secondary structures. […]


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RNA Sampler institution(s)
Department of Genetics, Washington University, School of Medicine, St Louis, MO, USA

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