RNAshapes protocols

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RNAshapes specifications

Information


Unique identifier OMICS_03466
Name RNAshapes
Alternative name RNA shapes studio
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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Information


Unique identifier OMICS_03466
Name RNAshapes
Alternative name RNA shapes studio
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for RNAshapes

library_books

The RNA shapes studio.

2015 Bioinformatics
PMCID: 4308662
PMID: 25273103
DOI: 10.1093/bioinformatics/btu649

RNAshapes in pipelines

 (5)
2011
PMCID: 3293930
PMID: 22051375
DOI: 10.1186/1471-2105-12-429

[…] models of the rna folding space, named nodangle, overdangle, microstate and macrostate. they capture four different models of the folding space, as they are implemented in the programs rnafold[], rnashapes[], and rnasubopt[].1 we compare the outcome of predictions from the different models, and evaluate them against three data sets derived from experimentally proved structures., the goal […]

2011
PMCID: 3293930
PMID: 22051375
DOI: 10.1186/1471-2105-12-429

[…] with correct energies, and without redundancy., this answers the questions raised at the outset of this study., our evaluation has concentrated on the models underlying the programs rnafold, rnashapes, and rnasubopt. there are many other folding programs out there. if these implementations adhere to the abstract models we present here in the form of tree grammars, our evaluation pertains […]

2011
PMCID: 3293930
PMID: 22051375
DOI: 10.1186/1471-2105-12-429

[…] assumptions and model simplifications used by the programs on the outcome of the analysis., we extract four different models of the thermodynamic folding space which underlie the programs rnafold, rnashapes, and rnasubopt. their differences lie within the details of the energy model and the granularity of the folding space. we implement probabilistic shape analysis for all models, […]

2010
PMCID: 2828121
PMID: 20080511
DOI: 10.1093/bioinformatics/btq014

[…] structural data via machine learning techniques. to benefit from our aproach, these methods need to be augmented to support shape abstraction. technically, they are based on different grammars than rnashapes. for these grammars, shape abstraction functions need to be defined and implemented. then, our tdm generator and the strategies described here should carry over without change., the authors […]

2005
PMCID: 1261154
PMID: 16156887
DOI: 10.1186/1471-2105-6-224

[…] training a generation of students on the concepts presented here, we have enjoyed a boost in programming productivity. four bioinformatics tools have been developed using this approach -pknotsrg [], rnashapes [], rnahybrid [] and rnacast []. the "largest" example is the pseudoknot folding grammar, which uses 47 nonterminal symbols and a 140-fold case distinction. the techniques described […]


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RNAshapes in publications

 (51)
PMCID: 5848454
PMID: 29529991
DOI: 10.1186/s12859-018-2091-8

[…] methods such as icshape [] that can determine rna structures, rna structure data is not captured in most experimental methods, and it is usually predicted from sequence data using algorithms such as rnashapes [] and rnaplfold []. given the experimental data as input, a number of computational methods have been developed to build binding preference models. those methods can be roughly classified […]

PMCID: 5836418
PMID: 29506466
DOI: 10.1186/s12859-018-2078-5

[…] unimodal. this has led to efforts to find clusters of structures when no single representative structure exists. methods include standard clustering algorithms [–] and strategies tailored to rna ss: rnashapes [–] finds structures that share a common “shape”, and rogers et al. [] group structures that share common helices in a process called “profiling”. both of these strategies simplify the rna […]

PMCID: 5819699
PMID: 29463232
DOI: 10.1186/s12864-018-4540-1

[…] sequences, all based on a position-independent uniform distribution of nucleotides. to measure the probability of a probe being unstructured, we followed the definition of ray et al. []. we ran rnashapes version 2.1.6 in the following way: “rnashapes -s -c 70.0 -r -m 30 -t 1 -o 2 “[]. the reported probability is one minus the sum of probabilities of structures below − 2.5 kcal/mol […]

PMCID: 5577171
PMID: 28855631
DOI: 10.1038/s41598-017-10318-w

[…] braf, foxe1, igf1, nkx2-1, ntrk1, ntrk2, pax8, rara, rarb, ret, slc26a4, slc5a5, slc5a8, tg, tgfb1, thra, thrb, tp53, tpo, tshr., the structure of the putative novel mir-tg was analyzed using rnashapes (vienna rna package, version 1.5) and rna structure 5.3 (university of rochester medical center mathews lab) to assess if the putative pre-mirna hairpin meets the criteria of minimum free […]

PMCID: 5545994
PMID: 28786034
DOI: 10.1186/s12284-017-0177-y

[…] into cis and trans ones. additionally, if the srna-seq data is available, phase-distributed nat-sirnas could be identified from the predicted nats by using natpipe., rnafold (hofacker, ) and rnashapes (steffen et al., ) are both easy-to-use tools for local rna secondary structure predictions. rnafold is a web server allowing a query sequence of up to 10,000 nt in length, but its graphic […]


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RNAshapes institution(s)
Practical Computer Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany; Practical Computer Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany

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