Section: Software and Platforms

Varna

Participants : Yann Ponty [correspondant] , Alain Denise.

Varna is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. Varna implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing, either as a bitmap (JPEG, PNG) or as a vector picture (SVG, EPS and XFIG). It also allows manual modification and structural annotation of the resulting drawings using either an interactive point and click approach, within a web server or through command-line arguments. Varna is a free software distributed under the terms of the GPLv3.0 license and available at http://varna.lri.fr .

Varna is currently used by RNA scientists (Cited by 92 research articles since its presentation in Fall of 2009, according to Google scholar), web servers such as the BouldeAle (http://www.microbio.me/boulderale/ ), TFold (http://tfold.ibisc.univ-evry.fr/TFold/ ), CyloFold (http://cylofold.abcc.ncifcrf.gov/ ) webservers, and by databases such as IRESite (http://iresite.org/ ), sRNATarBase (http://ccb.bmi.ac.cn/srnatarbase/ )and Rfam (http://rfam.sanger.ac.uk/ ), the main source of sequence/structure data for RNA scientist, to display secondary structures. It is also used as an integrated component within JalView , arguably one of the leading sequence alignment editor (http://www.jalview.org/ ), and Y. Ponty co-supervised with Jim Procter (University of Dundee, Jalview Project Leader) two internships (including a Google Summer of Code) in the summer of 2012 to further the interactions between the two software.