BIOINFORMATICS APPLICATIONS NOTE
Vol. 25 no. 15 2009, pages 1974–1975
VARNA: Interactive drawing and editing of the RNA
Kévin Darty1, Alain Denise1,2and Yann Ponty1,3,∗
1LRI, UMR CNRS 8623,2IGM, UMR CNRS 8621, Université Paris-Sud 11 F91405 Orsay cedex and3Génomique
Analytique, INSERM U511, 75013 Paris, France
Received on December 15, 2008; revised and accepted on April 7, 2009
Advance Access publication April 27, 2009
Associate Editor: Ivo Hofacker
visualization and annotation of the secondary structure of RNA,
designed as a companion software for web servers and databases.
Features: 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.
Availability: VARNA is a free software, released under the terms of
the GPLv3.0 license and available at http://varna.lri.fr
Supplementary information: Supplementary data are available at
With the increasing interest in structure-based methods for the
analysis of RNA, many web servers now provide tools ranging
from the detection of non-coding RNAs (Washietl et al., 2005) to
the rational design of small interfering RNAs (Ding et al., 2004).
In parallel, databases listing RNA secondary structures associated
with specific functions (Mokrejs et al., 2006), or obtained through
specific methods (Cannone et al., 2002), are increasing rapidly in
Various tools have been proposed for the clear visualization of
the results of such methods, and to produce publication-quality
pictures of RNA. However, most available applications either rely
on a specific operating system (OS) and/or third-party libraries,
or do not allow any user interaction (command-line tools). A
visualization application is therefore needed that: can be easily
standalone application; is platform-independent and free of external
dependencies; enables user-interaction; and exports publication-
quality pictures of edited/displayed RNA structures.
Thus, we developed VARNA (Visualization Applet for RNA), a
JAVA-based system implementing classic RNAdrawing algorithms
coupled with a set of edit/export/annotate features, allowing
publication-quality pictures to be created and displayed.
∗To whom correspondence should be addressed.
VARNA can be used in three different ways: as a standalone JAVA
through the HTML param applet option; or as a component that
can be included in any JAVAsoftware requiring a surface to display
and annotate the secondary structure of RNA. A fully documented
application programming interface (API) is provided for interfacing
our software from within existing software.
VARNA accepts most file formats traditionally used for the
notation (Washietl et al., 2005) (.dbn), MFold connect (Markham
and Zuker, 2005) (.ct), Gutell’s CRW format (Cannone et al., 2002)
(.bpseq) and the unifying RNAML (Waugh et al., 2002). With the
exception of RNAML, only accepted for input, each other format
is supported both for input and output, allowing for file format
conversions. Additionally, the software can process and display
structures featuring non-canonical base pairs (RNAML) and/or
VARNA can export the resulting drawing to a variety of graphic
formats, both pixel-based—Portable Network Graphics (PNG) or
Vector Graphics (SVG) and XFIG. Although the resolution and
compression level can be specified for pixel formats, vector
formats should be chosen for the production of publication-quality
drawings, as they allow further editing with third-party vector-
graphics software without any loss of quality. Generic libraries for
to be used within a minimal environment (no external software
required), while remaining as lightweight as possible (no bundled
VARNA implements four distinct algorithms (Figure 1) to draw
the secondary structure of RNA in one of its three usual
representations: the linear representation draws the backbone on
a straight line and connects paired bases with arcs; the Feynman
diagram-like circular representation draws the backbone on a
circle, while connecting partners with chords; the planar graph
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
RNA drawing with VARNA Download full-text
Fig. 1. Four representations (Radial, Circular, Linear and NAView) of
the GAG-Pol -1 frameshift-inducing element in HIV-1 (PDBID:1ZC5) as
rendered by VARNA under default settings.
bases, while limiting the structural overlap. We implemented two
algorithms for the planar graph representation. The radial strategy
draws each helix and base in a multiloop at regular angular
distances, as done by RNAViz (Rijk et al., 2003). This gives
a drawing which is potentially self-intersecting, but allows for
richer user interactions. Additionally, the exterior loop can be
aligned to a baseline in this representation. The NAView drawing
algorithm (Bruccoleri and Heinrich, 1988) uses a heuristic approach
to generate a non-intersecting representation of the RNA secondary
Non-canonical base pairs can be read from an RNAML file
and displayed using standard notations defined by the Leontis–
Westhof classification system (Leontis and Westhof, 2001). Other
be the preferred choice.
Partial support for pseudoknots is also provided by VARNA.
Upon loading a pseudoknotted secondary structure, a maximal non-
crossing subset of its base pairs is extracted using a dynamic
programming algorithm (Xayaphoummine et al., 2003). The
resulting secondary structure is then used as a scaffold for additional
base pairs, resulting in a planar graph representation.
Non-canonical base pairs/pseudoknots
VARNA users can modify an automatically drawn structure using
basic interactions. Namely, structures drawn using the radial
algorithm can be modified by rotating or flipping (exterior loop
featured only) an helix, together with all its subsequent elements,
around the center of its supporting loop, allowing manual removal
of potential self-intersections. The other drawing algorithms offer
the possibility of post-editing modifications by means of moving
single bases (NAView or circular) or base pairs (planar).
VARNA also offers base and base pair annotation features,
allowing selected bases, base pairs or any structural element (Helix,
loop, stem, etc.), chosen from a contextual menu, to be highlighted
and/or annotated. Once these elements are selected, individual bases
and base pairs can be customized to highlight a region of interest.
As an applet, most features offered by VARNA can be accessed
through HTML param tags. This allows a web server to
benefit from VARNA’s visual impact, as previously shown for the
IRESite (Mokrejs et al., 2006), using a previous version of our
software. Additionally, the VARNA applet can render several RNA
structures simultaneously, allowing a visual comparison of RNA
structures, as previously shown with the NestedAlign (Blin et al.,
2008) web server (http://nestedalign.lri.fr/). User interactions can be
restricted to circumvent undesired modifications.
Web server features
A version (1.5+) of the JAVA plugin is required to run VARNA.
referees for helpful suggestions during early stages of VARNA’s
Funding: ANR projects BRASERO ANR-06-BLAN-0045 and
Conflict of Interest: none declared.
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