RnaViz 2: an improved representation of RNA secondary structure

Summary: RnaViz has been developed to easily create nice, publication quality drawings of RNA secondary structure. RnaViz 2 supports CT, DCSE, and RNAML input formats and improves on many aspects of the first version, notably portability and structure annotation. RnaViz is written using a hybrid programming approach combining pieces written in C and in the scripting language Tcl/Tk, making the program very portable and extensible. Availability: Source code, binaries for Linux and MS Windows, and additional documentation are available at http://rrna.uia.ac.be/rnaviz/ Contact: derijkp@uia.ua.ac.be Several formats for storing RNA secondary structure information exist that are not really suitable for eyeball comparison and publication of structures. A new version of RnaViz (De Rijk and De Wachter, 1997) is presented. RnaViz 2 will read files containing the secondary structure, extract the structure information, and automatically draw the structure contained in the file. The structure drawings can then be edited and annotated into publication quality 2D drawings. RnaViz supports reading files in the DCSE (De Rijk and De Wachter, 1993) format that incorporates special symbols indicating the secondary structure in an RNA sequence alignment. It can also read CT files as produced by the mfold program (Jacobson and Zuker, 1993). The detection of helices in CT files has become more advanced: helices consisting of several segments will now be detected as one helix, reducing clutter and improving layout. The new version also supports loading RNAML (Waugh et al., 2002) formatted files. RNAML is a new XML-based format for storing RNA structure. Some of these formats can contain more than one structure; in this case, the user can select to either draw a number of these structures on one page, or batch process them into different pages. Structure drawings are by default saved in the new, more efficient file format, although loading of files in the old format is