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Section: Software and Platforms

RNA tools – RNA structure prediction and comparison


Actively maintained/Actively developed

Inria Evaluation Committee Criteria for Software Self-Assessment: A-4, SO-3, SM-2, EM-3, SDL-4, DA-4, CD-4, MS-4, TPM-4

The RNA tools provide a suite of programs to help analysing RNA secondary structures, together with visualisation tools for RNA 2D structures and RNA multiple alignments. Our first tool was carnac for RNA structure prediction by comparative analysis. carnac was issued in 2004 (CARNAC: folding families of related RNAs. H. Touzet et al., Nucleic Acids Research, 2004), independently benchmarked (A comprehensive comparison of comparative RNA structure prediction approaches. P. Gardner et al., BMC Bioinformatics, 2004), and re-designed in 2009. It is still cited and used. Over the years, we have add new programs: regliss for locally optimal secondary structures, gardenia for structure comparison, CG-seq for gene prediction by comparative analysis, ...