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

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Documentation


Maintainer


  • person_outline Loren Dean Williams <>

Publication for RiboVision

RiboVision in publications

 (4)
PMCID: 5829716
PMID: 29309687
DOI: 10.1093/nar/gkx1308

[…] 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 ()., non-modified synthetic rna oligoribonucleotides were purchased from microsynth (balgach, switzerland). synthetic rna oligoribonucleotides containing oxidized rna residues […]

PMCID: 4753503
PMID: 26876483
DOI: 10.1038/srep20885

[…] homo sapiens were obtained from protein data bank.structures were superimposed pairwise using pymol “super” command with default settings., shape data are normalized and mapped on in-house ribovision server using the custom data function., shannon entropies were calculated as previously described., figures of three-dimensional structures are prepared with pymol or maxon cinema 4d […]

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

[…] are presented as pairs of base pairs. 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)., rna secondary (2°) structures, with symbolic representations of base pairs, double-helices, loops, bulges, and single-strands, […]

PMCID: 3753638
PMID: 23771137
DOI: 10.1093/nar/gkt513

[…] 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 ()., to build the best 2° structural model of the 23s rrna, we defined helices […]


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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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