Rat Genome Database (RGD)

Rat Genome Database (RGD) provides integrated curated rat genetic and genomic data (genes, quantitative trait loci (QTL), microsatellite markers, and rat strains) and comparative genomics and annotation tools to support translational and genomic research using rat models.

Key Features:

• Data Integration and Curation: Consolidates curated data on rat genes, quantitative trait loci (QTL), microsatellite markers, and rat strains via literature curation and bulk dataset updates.
• Comparative Genomics (VCMap): Provides comparative genomics tools including VCMap to view mapped genes and sequences across rat, mouse, and human genomes for cross-species comparison.
• Disease-Centric Resources: Maintains disease portals that unify genes, QTL, and strain models related to neurological and cardiovascular diseases across rat, mouse, and human.
• Ontology and Annotation Systems: Implements gene ontology, disease, pathway, and phenotype annotations to represent and link biological knowledge.
• Data Mining and Analysis Tools: Offers tools for data mining and analysis to survey datasets and identify candidate genes associated with disease phenotypes in rat models.
• Genomic Sequence Integration: Incorporates the rat genomic sequence into database resources to improve mapping and annotation accuracy.
• Genomic Mapping and Marker Tools: Supports genetic mapping, gene prediction, radiation hybrid mapping, and polymorphic marker selection.

Scientific Applications:

• Biochemistry, Nutrition, Pharmacology, and Physiology: Provides annotated datasets and ontology-based information to support research in these physiological and biochemical domains using rat models.
• Translational Research: Enables cross-species comparisons and disease-portal-driven analyses to translate findings from rat models to human pathobiology.
• Genomic and Genetic Studies: Supplies datasets and tools for genetic mapping, gene prediction, radiation hybrid mapping, and polymorphic marker selection to facilitate genomic investigations.

Methodology:

Targeted literature curation emphasizes disease-relevant data for neurological and cardiovascular conditions; the rat genomic sequence is integrated into database resources; and tools such as VCMap are developed and enhanced.