VARNA: Interactive drawing and editing of the RNA secondary structure
Supplementary information:Supplementary data are available at Bioinformatics online.
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 number.
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 accessed from within a web server to display its results; operates as a 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
2 MAIN FEATURES
2.3 Drawing algorithms
2.4 Non-canonical base pairs/pseudoknots
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 representations, such as that used in RNAViz (Rijk et al., 2003), may be the preferred choice.
Partial support for pseudoknots is also provided by
2.6 Web server features
As an applet, most features offered by
A version (1.5+) of the JAVA plugin is required to run
The authors are grateful to M. Weber, D. Castillo and the anonymous referees for helpful suggestions during early stages of
Funding: ANR projects BRASERO ANR-06-BLAN-0045 and GAMMA 07-2_195422.
Conflict of Interest: none declared.
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