COMPARATIVE GENOMIC MAPPING TOOLSET AND DATABASE

National Center for Genome Resources, 1800A Old Pecos Trail, Santa Fe, New Mexico 87505 USA

Comparative genomics provides powerful techniques for scientific discovery. Well known methods include nucleotide and protein sequence similarity, taxonomy and phylogeny. Emerging approaches include comparative analyses of physical and/or genetic maps. Many existing databases like RiceGenes, MaizeDB, SoyBase, BeanGenes and UK CropNet provide high quality maps and displays, but only RiceGenes and UK CropNet currently support comparative mapping. Because the focus of each database is specific to one or a few species, comparison possibilities are limited to the maps of other species selected by their curation groups and annotated with object relationships reported to them: Interspecies relationships are consequently static, and user directed discovery is not possible. In an effort to enable a wider, more dynamic range of interspecies map comparisons, the National Center for Genome Resources is developing a Comparative Genomic Mapping Toolset and Database. The database will incorporate mapping data from existing genome databases, leveraging the knowledge gained from the most rapidly advancing genome projects. It will support remote curation to promote timely access to quality data, and to allow easy introduction of map data for new species. The toolset will provide display capabilities for genetic maps, quantitative trait localizations and physical maps for individual species, pairs and sets. For comparative mapping, the system will empower the user to discover, display and retain relationships between map objects (loci, clones, ESTs, etc.) from different species based on nomenclature, sequence similarity, common motifs or other algorithmic methods.