RNAstrand statistics

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RNAstrand specifications

Information


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

Maintainers


  • person_outline Peter F. Stadler <>
  • person_outline Kristin Reiche <>

Information


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
Requirements
Vienna RNA package, LIBSVM library
Maintained No

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Publication for RNAstrand

RNAstrand in publications

 (7)
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), […]

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

[…] 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 […]

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 […]

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

[…] 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., the observed results where plotted […]

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

[…] the search in three non–terminals may be worthwhile, especially since kh99 contains only 3 non–terminals, it was far from computationally feasible for the purposes of this paper., 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 […]


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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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