JAVA TOOLS FOR PLANT GENOME MAPPING

¹ Department of Applied Computing University of Dundee Dundee DD1 4HN Scotland

² Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland

The rapid increase in the volumes of data brought by new technologies, have increased the pressure to develop new software tools to efficiently map and visualize genomic data. The Scottish Crop Research Institute (SCRI) and the Department of Applied Computing at the University of Dundee are collaborating in the development of bioinformatics software designed for the generation and visualization of high-density linkage maps.

Currently we have two prototype tools under development:

GenoDisplay is a viewer and editor for recombination data. It incorporates a Quick and Dirty Mapping algorithm based on pattern matching of recombination data that allows significant volumes of new marker data to be rapidly incorporated into mature well-populated linkage maps. The file format is compatible with Joinmap.

Map3D provides a three-dimensional, interactive display of multiple linkage maps to allow visualization of large volumes of map data on a single display. Based on user-provided rules, links between common loci in linkage maps can be generated and displayed. It is also possible to view only selected subsets of the data. The user has the option of manipulating the interactive display in 3D space, in order to obtain the best view for analysis and/or presentation of the data.

Both applications are written as Java 1.2 applications/applets. Map3D uses the Java3D extension. They will operate on a range of platforms including Windows 95/98/NT, Mac and Unix. Both software tools together with example data sets will be available for distribution from http://www.scri.sari.ac.uk/bioinformatics