RnaViz

Purpose

The secondary structure of an RNA molecules is being studied using experimental, thermodynamical and comparative methods. These analyses produce data about connections, or alignments with extra information about the structures. However, an RNA structure can be most easily understood by visualising it in a 2D structure drawing. RnaViz is a program to produce pleasing, publication-ready structure drawings starting from the connection data (ct format as produced by mfold) or alignments with extra structure inforation (DCSE format).
RnaViz is more picky about the position of the helix names that DCSE: the helix name used is the first one on the helix numbering line after the postion where the strand of the helix is opened. (DCSE did check the strands before and after the helix name; this will also change in future versions of DCSE.)

Features

Some of the features special to RnaViz are:
  • recognises ct and DCSE alignment formats
  • multiple structures on page
  • simple but powerfull WYSIWYG editing using different selection modes
  • allows display of pseudoknots
  • free choice of fonts, colors, linewidths for any object
  • some graphics functions (rectangle, oval, lines, text)
  • linking of graphics, text to certain bases
  • tag based changing of properties
  • skeleton approach
  • automatic sequence numbering
  • zoom
  • independend scaling of structure drawings
  • portable
  • Starting RnaViz

    Starting RnaViz will display a page surrounded by scroll bars, a menu, a main toolbar, a secondary toolbar and a sidebar. All functions in RnaViz can be started from the menu, or using user-defineable key-shortcuts. Often used functions can be started from the toolbars. The menu and the key-shortcuts can be completely customised.

    Opening files

    The file menu contains an 'Open' entry. This will open a file selection box, in which a file to be loaded can be specified.

    If this file is an RnaViz structure file, the structures in that file will be loaded on the page. Structures already on the page will remain fully editable. They can be deleted by selecting them (click on one of their bases) and use the 'Delete object' option of the Edit menu (or just press delete). To remove all structures from the page the 'Clear Page' option in the File menu can be used.

    RnaViz will also recognise files in the ct or DCSE alignment format. A DCSE alignment should at least contain one sequence line (with structure symbols) and a "Helix numbering" line. Optionally a "mask" line can be present; the letters in the mask line will be associated as tags to the base on the same position.
    WARNING: the secondary structure parser in RnaViz is somewhat pickier about the location of helix numbers in the DCSE alignment format than versions of DCSE <4, eg. the helix number must always come on a position after the helix opening symbol ([) in a sequence.

    If the file is in the ct or DCSE alignment format, the user is prompted for a skeleton file. This is a file containing the layout of the structural elements in a previously made, structuraly similar drawing. The use of skeleton files makes it very easy to create a lot of drawings using the same layout. If this dialog is closed without choosing a skeleton file, no skeleton is used. Since RnaViz does not try to produce non overlapping drawings, a structure drawing produced without a matching skeleton file will usually take more manual laying out afterwards. Once a structure of a certain molecule has been layed out, it's skeleton can be saved and used for similar molecules.

    All structures in the file can be loaded straight into the same page, or as a batch job saving each structure to a different file.

    Editing a structure

    A structure on the page can be rearranged by clicking on one of its bases, and dragging this to a different position. When the base is released, the neigboring bases will also be moved so as to maintain a pleasing view. If the distances between the bases reaches a given treshhold, they will be automatically connected by a line.

    Depending on the selection mode, selecting a base can cause the helix segment or the entire helix the base is part of to be selected as well. Event the entire tree starting from this helix can be selected this way.

    The selected part of a structure can be rotated, flipped or redrawn. Single stranded areas can be straighthened or arched or drawn unformatted.

    Functions and options

    An overview of the functions found in RnaViz can be found in the contents.

    Implementation

    RnaViz is implemented using a combination of Tcl/Tk and C. It uses Tcl v8.0 and Tk v8.0. It also relies on the Extral and ClassyTk extensions. The C code mainly implements some of the numerical calculations. The interface and other parts of the calculations is written in Tcl.

    More information

    More information about new releases, bug fixes, etc. should appear on the rRNA web server (http://rrna.uia.ac.be/rnaviz/).

    How to contact me

    I will do my best to reply as fast as I can to any problems, etc. However, the development of extraL is not my only task, which is why my response might not be always as fast as you would like.

    Peter De Rijk
    University of Antwerp (UIA)
    Department of Biochemistry
    Universiteitsplein 1
    B-2610 Antwerp

    tel.: 32-03-820.23.16
    fax: 32-03-820.22.48
    E-mail: derijkp@uia.ua.ac.be
    web: http://rrna.uia.ac.be/~peter/personal/peter.html

    Legalities

    RnaViz is Copyright Peter De Rijk, University of Antwerp (UIA), 1997. The following terms apply to all files associated with the software unless explicitly disclaimed in individual files.

    The author hereby grants permission to use, copy and distribute this software and its documentation,provided that it is delivered with ALL the supplied files and UNALTERED, and it is not supplied on a disc you are charging for (except for media and postage costs). You can modify this software for personal use. If you want to distribute modified versions of this software or include it in a larger package, the author should be contacted.

    IN NO EVENT SHALL THE AUTHOR OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

    THE AUTHOR AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.