RNAstructure statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RNAstructure
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Tool usage distribution map

This map represents all the scientific publications referring to RNAstructure per scientific context
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Associated diseases

This word cloud represents RNAstructure usage per disease context
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Popular tool citations

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Protocols

RNAstructure specifications

Information


Unique identifier OMICS_03455
Name RNAstructure
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 5.8.1
Stability Stable
Registration required Yes
Maintained Yes

Subtools


  • AccessFold
  • AllSub
  • bifold
  • bipartition
  • CircleCompare
  • ct2dot
  • CycleFold, TurboKnot
  • dot2ct Draw
  • DuplexFold
  • Dynalign II
  • efn2
  • EnsembleEnergy
  • Fold
  • oligoscreen OligoWalk
  • partition
  • PARTS
  • ProbablePair
  • RemovePseudoknots
  • stochastic TurboFold

Download


conda.png

Versioning


No version available

Maintainer


  • person_outline David H. Mathews

Additional information


http://rna.urmc.rochester.edu/RNAstructureHelp.html http://rna.urmc.rochester.edu/RNAstructureWeb/Information/Help.html

Information


Unique identifier OMICS_03455
Name RNAstructure
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Stability Stable

Subtools


  • AccessFold
  • AllSub
  • bifold
  • bipartition
  • CircleCompare
  • ct2dot
  • CycleFold, TurboKnot
  • dot2ct Draw
  • DuplexFold
  • Dynalign II
  • efn2
  • EnsembleEnergy
  • Fold
  • oligoscreen OligoWalk
  • partition
  • PARTS
  • ProbablePair
  • RemovePseudoknots
  • stochastic TurboFold

Maintainer


This tool is not maintained anymore.

Additional information


http://rna.urmc.rochester.edu/RNAstructureHelp.html http://rna.urmc.rochester.edu/RNAstructureWeb/Information/Help.html

Publications for RNAstructure

RNAstructure citations

 (338)
library_books

RNA Pull down Procedure to Identify RNA Targets of a Long Non coding RNA

2018
PMCID: 5933463
PMID: 29708552
DOI: 10.3791/57379

[…] Using the primary sequence of the lncRNA of interest, generate its secondary structure on the "RNAstructure Webserver". NOTE: On this site, different algorithms can be used. The three prediction tools that give the best results for the probe designs are: "Fold" (lowest free energy structure), " […]

library_books

Ribosome dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE

2018
Sci Rep
PMCID: 5882922
PMID: 29615727
DOI: 10.1038/s41598-018-23845-x

[…] The RNA secondary structure of the IRES element under different conditions was predicted using RNAstructure imposing SHAPE reactivity values as pseudo-free energy change constraints together with nearest neighbor thermodynamic parameters using -0.8 kcal/mol and 2.6 for the intercept (b) and slo […]

library_books

Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants

2018
Mol Plant
PMCID: 5886760
PMID: 29409859
DOI: 10.1016/j.molp.2018.01.008

[…] ree energy function (). Their CDS were folded as well. The phylogenetic structure of 18S rRNA was downloaded from the Comparative RNA Web site (http://www.rna.icmb.utexas.edu/). The scorer utility in RNAstructure (RNAstructure-5.8.1) was used for PPV and sensitivity calculation. The F1 score was calculated from the previous definition (). When comparing PPV in CDS between rice and Arabidopsis, mRN […]

library_books

An RNA binding compound that stabilizes the HIV 1 gRNA packaging signal structure and specifically blocks HIV 1 RNA encapsidation

2018
Retrovirology
PMCID: 5853050
PMID: 29540207
DOI: 10.1186/s12977-018-0407-4

[…] as described previously []. Outliers were defined as above and were removed from the dataset. These constituted less than 8% of values. The average reactivities were then used as SHAPE constraints in RNAstructure [] to predict structural models and their free energies. […]

library_books

The Expansion Segments of 28S Ribosomal RNA Extensively Match Human Messenger RNAs

2018
Front Genet
PMCID: 5850279
PMID: 29563925
DOI: 10.3389/fgene.2018.00066

[…] Predictions of oligoribonucleotide and polyribonucleotide secondary structures were obtained with RNAstructure program (Mathews et al., ) and with RNAfold program (Gruber et al., ). These programs were also used for modeling the free energies of secondary structure formation/disbanding. […]

library_books

Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory

2018
BMC Bioinformatics
PMCID: 5836418
PMID: 29506466
DOI: 10.1186/s12859-018-2078-5

[…] e fact that secondary structure prediction algorithms struggle to provide accurate predictions for some of the longer sequences considered. If we rerun the analysis on the 309 5s RNA sequences in the RNAstructure test set, we find that the average native cluster size is 41.5% – significantly higher than the mean random cluster size of 37.0% (permutation p-value = 0.02). However it is still far sho […]


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RNAstructure institution(s)
Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA; Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA; Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
RNAstructure funding source(s)
Supported by National Institutes of Health (NIH) [R01 GM076485].

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