RAT GENOME DATABASE

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The rat is a widely-used and highly-valued model system for physiology, pharmacology, and toxicology. The US and International Rat Genome Projects have developed new genomic tools and resources. The information and reagents developed through these efforts has grown at an astounding pace. More than 8,000 genetic markers cover the rat genome, and hundreds of known genes are placed within this genetic framework. Multiple large- insert genomic libraries, radiation hybrid (RH) cell lines and map, normalized cDNA libraries, allele characterization for genetic markers in 48 inbred strains, a cytogenetic map, over 90,000 ESTs (2,000 of them mapped), and comparative maps have been generated. However, the support for the database infrastructure has been limited. Currently, data are distributed across many databases at scores of research labs, and many important data sets are not available on the internet. We propose the following specific aims: 1. Address the immediate community-wide need for a publicly available rat genomic database currently available (http://www.informatics.jax.org/rat),while we transition to RGD. 2. Populate the RGD with data in the following areas: ESTs, genes, markers, primer names, genetic maps and comparative maps and supporting homology information (TJL), and UniGene Clusters. 3. Implement the RGD curation system and supporting data structures to allow direct data entry and editing by project staff and downloads of bulk data from genome centers. 4. Provide a rat RH reference map that is integrated with collections of EST and genetic markers. 5. Provide on-line tools for using the resources of the rat genome. 6. Promote the use of RGD as a tool for data analysis and exploration by providing user training and on-line help, by responding to user queries, and by community outreach activities, such as a visiting scientists training program.