Software

  • VARNA

    Visualisation Applet for RNA.
    A lightweight Java Applet dedicated to the quick drawing of an RNA secondary structure. VARNA is opensource and distributed under the terms of the GNU GPL license. Automatically scales up and down to make the most out of a limited space. Can draw multiple structures simultaneously. Accepts a wide range of documented and illustrated options, and offers editing interactions. Exports the final diagrams in various file formats (svg,eps,jpeg,png,xfig) ..
    VARNA currently ships in its 3.9 version, and consists in 50 000 lines of code in 250 classes.
    Availability: distributed under the terms of the GPL v3 licence since 2009 on simple demand to the author(s)
    at http://varna.lri.fr
    Impact: Downloaded 10k+ times and is cited by more than 270+ research manuscripts (source: Google Scholar).
    Correspondant: Yann Ponty

  • GenRGenS

    Generation of Random Genomic Sequences and Structures
    A software dedicated to the random generation of sequences. Supports different classes of models, including weighted context-free grammars, Markov models, PROSITE patterns… Details. GENRGENS currently ships in its 2.0 version, and consists in 25 000 lines of code in 120 Java classes.
    Availability: distributed under the terms of the GPL v3 licence since 2006 on simple demand to the author(s)
    Impact: Downloaded 5 000 times and is cited by more than 60+ research manuscripts (source: Google Scholar).
    Correspondant: Y. Ponty

  • DiMoVo

    DIscriminate between Multimers and MOnomers by VOronoi tessellation
    Knowing the oligomeric state of a protein is necessary to understand its function. This tool provides a reliable discrimination function to obtain the most favorable state of proteins. Bibliography.
    Availability: released in 2008. Maintained.
    Correspondant: Julie Bernauer

  • VorScore

    Voronoi Scoring Function Server.
    Scoring is a crucial part of a protein-protein procedure and having a quantitave function to evaluate conformations is mandatory. This server provides access to a geometric knowledge-based evaluation function. It is still maintained and widely used. Bibliography.
    Availability: released in 2007.
    Correspondant: Julie Bernauer