rNAV 2.0 – Visual Exploration of sRNA mediated Regulatory Network

rNAV 2.0

:: DESCRIPTION

rNAV (for rna NAVigator), is a major evolution of rNAV, 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.

::DEVELOPER

Romain Bourqui

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

rNAV

:: MORE INFORMATION

Citation

Bourqui R, Dutour I, Dubois J, Benchimol W, Thébault P.
rNAV 2.0: a visualization tool for bacterial sRNA-mediated regulatory networks mining.
BMC Bioinformatics. 2017 Mar 23;18(1):188. doi: 10.1186/s12859-017-1598-8. PMID: 28335718; PMCID: PMC5364647.

RNAv – Search Genomes for RNA Secondary Structure Variation

RNAv

:: DESCRIPTION

RNAv (RNA secondary structure variation) is a program that searches for RNA secondary structure variations based on the notion of a structure graph to specify the consensus structure of an RNA family.The model for profiling the consensus structure of an RNA family is a conformational graph that specifies the topology of the consensus fold and relationship among helices and unpaired loops. Individual helices and loops are modeled with a restricted Covariance Model and profile HMM, respectively. The fold topology, helices, and loops are trained with an input pasta file that contains a multiple structural alignment for a set of training RNA sequences.

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Complier

:: DOWNLOAD

 RNAv

:: MORE INFORMATION

Citation

Huang, Z., Malmberg, R., Mohebbi M., and Cai, L. (2010)
RNAv: Non-coding RNA Secondary Structure Variation Search via Graph Homomorphism
Proceedings of Computational Systems Bioinformatics Conference (CSB 2010), August, 2010. Vol. 9, p. 56-69.