VARNA

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. Features: *Automatically scaled, anti-aliased Smooth rendering*Support provided for input files in BPSEQ, CT, Vienna (DBN: dot bracket notation) or RNAML formats*Export of snapshots in vector and bitmap picture formats: EPS, SVG, XFIG, JPG, or PNG.*Fully-customizable, through a documented API for the component, or a set of documented " "-type options for the Applet version*Platform and browser iNdependence (Only requires the installation of a version 1.5 of the Java plugin*Support of non-canonical basepairs using the Leontis/Westhof nomenclature. Pseudoknotted structures are processed by first extracting a maximal planar subset of canonical base-pairs, draw the subset and use it as a scaffold for the rest of the base pairings.*Provides real time user interaction and full display customization.*Displays multiple secondary structures on a single Applet, saving precious computational ressources.*Supports semi-automated annotation of individual structural parts, color maps and chemical-probing style of annotations.