Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Multidimensional Comparative Annotation Tool (MuDCAT): 3D Viewer For Comparing Multiple QTL Maps

Robert T Ball , Frank A Feltus , Barry S Marler , Andrew H Paterson

  Plant Genome Mapping Laboratory - University of Georgia, Athens, Georgia 30602, USA

The visualization of linear genomic annotation data is easily done with 2D visualization tools such as those found in GMOD (Stein et al 2002) and ENSEMBL (Cuff et al 2004) as well as a 3D implementation called SOCKEYE (Montgomery et al 2004). However, the n-wise comparison of multiple genomic annotations such as the visual comparison of multiple genetic or QTL maps becomes increasingly difficult in two dimensions when more than two comparisons are made. An excellent tool for the comparison of two maps is CMAP, a component of GMOD. In order to project multiple QTL maps for visualization, we have developed software (MuDCAT) that renders multiple QTL maps as an interactive 3D object that can be used to visualize overlapping QTLs (or other annotations). The software was written in C++ using the OpenGL graphics library. Input into the program is an XML file that is dumped from a CMAP database (see www.gramene.org for an example) which we have extended in a local CMAP installation to confer this functionality. Therefore, a user can query CMAP and visualize comparisons in a traditional 2D image as well as transfer the same data into MuDCAT. This software was written for Windows-based systems but a prototype Linux viewer is being developed in parallel.