Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Bioinformatics: Software
           Computer: Poster and Demo

GenomePixelizer - A VISUALIZATION TOOL FOR COMPARATIVE GENOMICS WITHIN AND BETWEEN SPECIES

¹ Department of Vegetable Crops, University of California at Davis, Davis, CA, 95616, USA

We developed a genome visualization program, GenomePixelizer, to study evolutionary patterns of specific gene families in whole genome(s). GenomePixelizer generates custom images of the physical or genetic positions of specified sets of genes in one or more genomes or parts of genomes. The positions of user-selected sets of genes are displayed along the chromosomes based on either physical or genetic distances. Multiple sets of genes can be shown simultaneously with user-defined characteristics presented. It allows the analysis of duplication events within and between species by displaying user-adjustable levels of sequence similarity. This provides comparisons between patterns of duplication for different families of genes, investigations of the occurrence of large versus local duplications and deletions as well as studies of macro- and micro-synteny. We are using GenomePixelizer to study the evolution of NBS-LRR encoding genes in comparison to other families of similar size such as cytochrome P450 and receptor kinase encoding genes in Arabidopsis both at the whole genome level and at the level of individual clusters. We are also adapting GenomePixelizer to display homologs identified in EST libraries for comparative studies. The program is written in Tcl/Tk and works on any computer platform that supports the Tcl/Tk toolkit. GenomePixelizer generates HTML ImageMap tags for each gene allowing links to databases. GenomePixelizer is under GNU General Public License. Detailed program description, more examples and documentation are freely available at: http://niblrrs.ucdavis.edu/GenomePixelizer/