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Genome-wide detection of sRNA targets with rNAV

rNAV (for rna NAVigator) is a tool for the visual exploration and analysis of bacterial sRNA-mediated regulatory networks. rNAV has been designed to help bioinformaticians and biologists to identify, from lists of thousands of predictions, pertinent and reasonable sRNA target candidates for carrying out experimental validations.

We now propose an automatic mRNAs extraction from a simple genbank or embl genome file. Moreover, rNAV now features an automatic annotation enrichement plugin powered by DAVID statistical enrichement tool.
rNAV algorithms can be gathered into pipelines which can then be saved and reused over several sessions. To support exploration awareness, rNAV also provides an exploration tree view that allows to navigate through the steps of the analysis but also to select the sub-networks to visualize and compare. These comparisons are facilitated by the integration of multiple and fully linked views.

This framework had been used to analyse various real biological data including several mycoplasma strains.

Some key features :

  • Automatic functional annotation with DAVID[1] webservice (Database for Annotation, Visualization and Integrated Discovery)
  • Annotation clustering : cluster redudant annotations
  • Simultaneous visual analysis of annotations AND positions of several targets with enhanced neighbors tool.
  • Visual analysis of sRNA regulatory networks at genome scale
  • Automatic mRNA extraction from genome files (genbank or embl) with user defined region
  • Integration of two interactions prediction tools : ssearch and IntaRNA[2]
  • Position clustering : cluster targets from their interaction positions
  • Multiple and fully linked view
  • Exploration tree view
  • Labels can display many input information like P-value, Similarity or interaction energy
Release Date:
Data type:
2D, Network / hierarchy graph
Tulip 3.8

Project development

Institution: Universite Bordeaux 1, Universite Bordeaux 2, Universite Paris 7, ANR (France)

This work was partially done under the EVIDEN project (ANR 2010 JCJC 0201 01), supported by the ANR (France); and under the MycoRNA project, PEPS CNRS/IdEx Bordeaux, 2013.