Our goal is to improve the diffusion, manipulation, storage and visualisation
of the RNA data. To do that, we develop informatic tools supporting the
RnaML file format.
|The RnaML file format|
In order to improve information exchange in biology, the XML format is now largely used in this field of research.
The RnaML syntax was designed to easily express data on RNA sequence and structure, and to allow the transmission of information among the RNA community. The syntax is the result of a collaborative effort between researchers active in the field of RNA structure and computer science.
|The RnamlView tool|
In order to easily view, analyze, manipulate and save rna data stored
in rnaml file format, we have designed a graphical viewer implemented with
the Java language. This viewer named RnamlView open a pdb or an rnaml file
and construct :
RnamlView is not able to calculate a secondary structure. It generates a dynamic representation of a secondary structure already stored in an RnaML file.
RnaView is a tool developed at the NDB laboratory (Rutgers University, NJ, USA). It generates a secondary structure from an Rna tertiary structure stored in a PDB file and identifies all the base pairs present in this structure. Therefore, the couple RnamlView-Rnaview allows to easily view and manipulate a Rna tertiary structure. All the base pairs found by RnaView are graphically represented with symbols in agreement with the LW classification.
You can find below a screenshot of RnamlView with :
The 1B and 2B panels will be used to give more informations on elements
selected on panels 1A and 2A respectively and to set properties for these
elements (color, value,...). These graphical widgets are functional but
are still under development.
With the File -> Open menu, you can open a PDB or an RnaML file. By opening a PDB file, RnamlView will call RnaView to generate the corresponding RnaML file which will be parsed by RnamlView.
You can save your work either as a complete RnaML file (File->save menu) or only the drawing as a PS or SVG file. The PS export is done by RnaView and the SVG export is done by RnamlView. SVG files can be opened with Adobe Illustrator 10 for example or inside a browser with the good plug-in. With SVG files inside Adobe Illustrator you can modify your drawing with special tools not provided by RnamlView.
To save, it's necessary to give the suffix of the type you want (.ps, .rnaml, .svg,...).
|The RnamlView symbols display and the LW classification|
In agreement with the RnaView output :
|Download and Installation|
To use RnaMLView, you need a 1.3 Java Platform installed on your system. RNAVIEW is provided as binary or source code so you can recompile it for your machine. RnaMLView and RNAVIEW have been tested and work fine under UNIX systems like Linux and MacOSX. To get the secondary structure from a pdb file, you need to be connected to Internet since the program need to parse the RnaML DTD stored at http://ndbserver.rutgers.edu/rnaml.dtd.
Download RnamlView, click the link : RnamlView_1.0-RnaView.tar.gz
Unpack the program package in your home directory (for example /home/skynet/share/) by typing :
tar -xzvf RnamlView_X.X-RnaView.tar.gz
That will create an RnaMLView directory on your system. It's important to put this directory where you have rights to write files. The RNAVIEW program uses temporary files to work.
The JAVA_HOME variable needs to be defined. This variable defines the directory where you have installed your Java platform.
Define the RNAMLVIEW environment variable corresponding to the directory you have just created.
export RNAMLVIEW=/home/skynet/share/RnamlView_X.X-RnaViewExample for tcsh shell:
setenv RNAMLVIEW /home/skynet/share/RnamlView_X.X-RnaView
Start the program
Run the rnamlview.sh script from the RnaMLView directory by typing: rnamlview.sh start (you can put the rnamlview.sh file in your PATH)
|For any problems or questions contact firstname.lastname@example.org|