RGD provides a variety of tools to search and analyze both the data within RGD and data generated from rat research in the lab. The list below identifies the major tools provided at RGD. Click a tool's name to start using the tool.
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Using a sequence name, gene name, locus, oligonucleotide (15 bp minimum) or other landmark you can search for its location on the rat genome. Links between the rat and human GBrowse facilitate cross-species comparisons. |
Using a sequence name, gene name, locus, oligonucleotide (15 bp minimum) or other landmark you can search for its location on the human genome. Links between the human and rat GBrowse facilitate cross-species comparisons. |
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Gviewer provides users with complete genome view of gene and QTL annotated to a function, biological process, cellular component, phenotype, disease, or pathway. The tool will search for matching terms from the Gene Ontology, Mammalian Phenotype Ontology, Disease Ontology or Pathway Ontology. |
SNPlotyper is a visualization and analysis tool for Rat SNP data. Containing data for over 400 strains and SNP data from multiple sources, it enables users to view haplotype blocks shared between strains and identify informative (polymorphic) markers between two or more strains. |
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 Overgo Probe Designer
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RatMine integrates data from RGD, UniProtKB, Ensembl, NCBI, PubMed and KEGG to form a web-based data warehousing, mining and analysis tool tailored to the needs of rat researchers. Datasets derived from querying this data or from uploading your own data can be saved, manipulated and/or downloaded for use in other applications. |
Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat-masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool allows users to submit their sequence of interest and get back optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends. |
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ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non-conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map |
The Virtual Comparative Map (VCMap) tool was originally developed to explore the syntenic relationships between rat, mouse and human genomes. A new version of VCMap is now available which also incorporates cow, pig and chicken, expanding both the versatility and utility of this valuable tool. |
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The Genome Scanner tool is designed to assist researchers in selecting polymorphic markers for a genome scan of a cross between two strains. It uses the Allele Characterization Project dataset in combination with various genetic and Radiation Hybrid maps. |
The Gene Annotator takes a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, and/or a chromosomal region, and retrieves annotation data from RGD. The tool will retrieve annotations from any or all ontologies used at RGD for genes and their orthologs, as well as links to additional information at other databases. |
