RiboVision statistics

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RiboVision specifications

Information


Unique identifier OMICS_18677
Name RiboVision
Software type Package/Module
Interface Web user interface
Restrictions to use None
Input data Data files, data syntax and data mapping.
Input format CSV
Computer skills Basic
Version 1.15
Stability Stable
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Drosophila melanogaster
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline Loren Dean Williams

Information


Unique identifier OMICS_18677
Name RiboVision
Software type Package/Module
Interface Command line interface
Restrictions to use None
Programming languages Javascript, PHP
License MIT License
Computer skills Advanced
Version 1.15
Stability Stable
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Drosophila melanogaster
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Loren Dean Williams

Publication for RiboVision

RiboVision citations

 (5)
library_books

Oxidative stress damages rRNA inside the ribosome and differentially affects the catalytic center

2018
Nucleic Acids Res
PMCID: 5829716
PMID: 29309687
DOI: 10.1093/nar/gkx1308

[…] ed via a moving mean window of 31. Therefore, the enrichment at every position was expressed as the mean of its own value and the 15 positions before and after. Oxidation heat maps were created using RiboVision (). […]

library_books

Frozen in Time: The History of Proteins

2017
Mol Biol Evol
PMCID: 5400399
PMID: 28201543
DOI: 10.1093/molbev/msx086

[…] s of LSU rRNAs are taken from our public gallery (http://apollo.chemistry.gatech.edu/RibosomeGallery, last accessed 24 February 2017). Data were mapped onto rRNA secondary structures with the program RiboVision (, online) (). […]

library_books

Ribosomal small subunit domains radiate from a central core

2016
Sci Rep
PMCID: 4753503
PMID: 26876483
DOI: 10.1038/srep20885

[…] SHAPE data are normalized and mapped on in-house RiboVision server using the custom data function. […]

library_books

Secondary Structures of rRNAs from All Three Domains of Life

2014
PLoS One
PMCID: 3914948
PMID: 24505437
DOI: 10.1371/journal.pone.0088222

[…] on a single sheet of standard sized paper. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision) .Our effort here is motivated in part by recent Cryo-EM structures of D. melanogaster and H. sapiens , which are extremely large, with […]

library_books

Secondary structure and domain architecture of the 23S and 5S rRNAs

2013
Nucleic Acids Res
PMCID: 3753638
PMID: 23771137
DOI: 10.1093/nar/gkt513

[…] base-stacking interactions were obtained from the library of RNA interactions (FR3D) () and confirmed by inspection and in-house code. Mapping of data onto 2° structures was performed on the in-house RiboVision server http://apollo.chemistry.gatech.edu/RiboVision. Images of 3D structures were generated with PyMOL (). […]

Citations

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RiboVision institution(s)
Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA; School of Biology, Georgia Institute of Technology, Atlanta, GA, USA; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA; Department of Computer Science, University of North Carolina at Charlotte, Charlotte, NC, USA
RiboVision funding source(s)
Supported by the NASA Astrobiology Institute (NNA09DA78A).

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