Section: New Software and Platforms

VARNA

Interactive drawing and editing of the RNA secondary structure

Keywords: Bioinformatics - Structural Biology

Scientific Description

VARNA is Java lightweight Applet dedicated to drawing the secondary structure of RNA. It is also a Swing component that can be very easily included in an existing Java code working with RNA secondary structure to provide a fast and interactive visualization.

Being free of fancy external library dependency and/or network access, the VARNA Applet can be used as a base for a standalone applet. It looks reasonably good and scales up or down nicely to adapt to the space available on a web page, thanks to the anti-aliasing drawing primitives of Swing.

Functional Description

Varna is a new 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 as five picture formats, either pixel-based (JPEG, PNG ) or vector-based (SVG, EPS and XFIG ).

It also allows manual modification and structural annotation of the resulting drawing using either an interactive point and click approach, within a web server or through command-line arguments.

• Participants: Alain Denise and Yann Ponty

• Partners: CNRS - Ecole Polytechnique - Université Paris-Sud

• Contact: Yann Ponty

• URL: http://varna.lri.fr/