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RNAstrand specifications


Unique identifier OMICS_23858
Name RNAstrand
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format CLUSTALW
License GNU General Public License version 3.0
Computer skills Basic
Maintained Yes


  • person_outline Peter F. Stadler
  • person_outline Kristin Reiche


Unique identifier OMICS_23858
Name RNAstrand
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Vienna RNA package, LIBSVM library
Maintained No


No version available


This tool is not maintained anymore.

Publication for RNAstrand

RNAstrand citations


Accurate Classification of RNA Structures Using Topological Fingerprints

PLoS One
PMCID: 5068708
PMID: 27755571
DOI: 10.1371/journal.pone.0164726

[…] of structures has greater than 50% sequence identity. Multiple families of the curated structures contain pseudoknots. While several large databases of RNA structures exist, for instance Rfam [] and RNAStrand [], these resources could not be directly used for testing in this work because many families lack pseudoknots, lack a consensus of expert opinion on the correct structure(s), have only a fa […]


Genome wide analyses of Epstein Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA

BMC Genomics
PMCID: 3751371
PMID: 23937650
DOI: 10.1186/1471-2164-14-543

[…] those that had at least one window with p-class > 0.9. When predictions had ambiguous strand orientations, e.g. occurred in a genome location that could be transcribed from either strand, the program RNAstrand [] was used to determine if structure was more likely to be in the forward or reverse strand.From each predicted locus the EBV-2 sequence was extracted and used in a BLAST [] search against […]


Quantifying variances in comparative RNA secondary structure prediction

BMC Bioinformatics
PMCID: 3667108
PMID: 23634662
DOI: 10.1186/1471-2105-14-149

[…] function of predictive accuracy for two single-sequence applications of RNA secondary structure prediction, RNAfold and PPfold (a recent implementation of Pfold, []), on 443 sequences taken from the RNASTRAND database []. Additionally, a uniform (0,1) cumulative density function is shown for comparison. The figure illustrates that for sequences in this data set, the predictive accuracy of RNAfold […]


Unrooted unordered homeomorphic subtree alignment of RNA trees

PMCID: 3765143
PMID: 23590940
DOI: 10.1186/1748-7188-8-13

[…] hem and reporting the relative score of their alignment. In each alignment mode m, where m ∈ {RO,RU,UO,UU}, we ran Algorithm 4, setting the input parameter dataset to all the structures from over the RNAStrand [] database (containing 1751 RNA structures), and setting the number of iterations (the amount parameter, in the code below) to 2 × 106. […]


CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Nucleic Acids Res
PMCID: 3627593
PMID: 23435231
DOI: 10.1093/nar/gkt101

[…] Because the entire RNAstrand data set is much bigger than the PDB data set (1987 versus 121 sequences), it allowed us to create subsets of sequences with different length ranges to evaluate the performance of individual […]


Evolving stochastic context free grammars for RNA secondary structure prediction

BMC Bioinformatics
PMCID: 3464655
PMID: 22559985
DOI: 10.1186/1471-2105-13-78

[…] We took data from RNASTRAND [], a collection of other databases [-]. We filtered the data set so that the sequences and structures could ensure reliability of predictions. We removed identical sequences and disregarded […]


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RNAstrand institution(s)
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Wien, Austria; Santa Fe Institute, Santa Fe, NM, USA
RNAstrand funding source(s)
Supported, in part, by the DFG Bioinformatics Initiative (BIZ-6/1-2) and the State of Saxony.

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