RGD Tools
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.
| The Virtual Comparative Map (VCMap) tool was developed to explore these syntenic relationships between Rat, Mouse and Human. VCMap enables investigators to link the physiology of rat with the genetics of mouse and the clinical significance of the human. |
This tool will run RHMAPPER and create a RH placement map of your submitted RH Vectors based on the 1999 RH Framework of the Rat. |
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| MetaGene is a powerful tool designed to provide exhaustive analysis of predicted gene features in sequence. It allows the researcher to submit sequences to seven gene prediction engines simultaneously to obtain a comprehensive report on sequence features. |
This 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. |
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| Annotations include Unigene, Gene, Homolog and other information. Users can enter a genome region to get all the types of data in this region with their genome map locations and annotaions, or submit a set of Genbank Names/Accession numbers to get their genome map locations and annotations. |
Using a sequence name, gene name, locus, oligonucleotide (15 bp minimum) or other landmark you can search for its location on the rat genome. |
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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. |
Using a sequence name, gene name, locus, oligonucleotide (15 bp minimum) or other landmark you can search for its location on the human genome. |
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| Use BLAT as an alignment tool to map submitted sequence to the genome, and annotate this region in visualization tools.. |
BLAST uses a heuristic algorithm to detect relationships among sequences which share regions of similarity. |
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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 |
This program provides a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked. |
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