Analysis & Visualization

RGD provides a variety of tools to search, analyze and visualize 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.

    JBrowse Genome Browsers     OLGA – Object List Generator & Analyzer
Genome browsers allow the user to view objects such as genes, variants, QTLs, and so forth in their genomic context.  RGD currently supports one genome browser. Click here for help getting started with RGD’s browsers or click one of these links to select your browser of choice:

Rat Bonobo Chinchilla
Mouse Dog
Human Squirrel
OLGA, the Object List Generator & Analyzer tool, is a straightforward list builder for genes from any of RGD’s species, for rat, human and mouse QTLs, or for rat strains, using any of a variety of querying options.  Find objects in RGD using genomic positions or any of RGD’s functional annotations, or enter your own list of symbols, then select how you want to use that list, e.g download the list to your own computer for analysis or loading into other tools, send the list to RGD’s GA Tool for functional analyses or, for rat, send the list to the Variant Visualizer to find strain-specific variants.
     InterViewer – Protein-Protein Interactions            Gene Annotator
InterViewer, RGD’s Cytoscape-based protein-protein interaction viewer, takes one or more UniProtKB protein IDs for rat, mouse, dog and/or human and displays pairwise protein interactions for them, with information about the types of interactions and links to the associated genes in RGD and the originating interaction records at IMEX 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.
    PhenoMiner     Variant Visualizer
The PhenoMiner Tool allows users to query and visualize quantitative phenotype data across rat strains and between studies. Begin by selecting rat strains, clinical measurements, measurement methods and/or experimental conditions to view and download the associated phenotype measurement data. Variant Visualizer is a viewing and analysis tool for rat strain-specific sequence polymorphisms and for human ClinVar variants.  Select samples of interest, define one or more genomic regions and, if desired, set parameters for the type(s) of desired variants and the tool will return all of the SNVs which match the input criteria, including information on read depth, zygosity and conservation score for rat variants, or clinical significance and associated phenotypes/diseases for human variants.
    Genome Viewer
RatMine integrates data on function, disease, phenotype, variation and comparative genomics 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. 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.
    ACP Haplotyper
     Overgo Probe Designer 
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 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.  PLEASE NOTE: the input sequence must be at least 10 KB.
    Genome Scanner
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.

Additional Tools Available Outside RGD (External Links)
BLAST uses a heuristic algorithm to detect relationships among sequences which share regions of similarity. Use BLAT as an alignment tool to map submitted sequence to the genome, and annotate this region in visualization tools.
  Repeat   Vega Browser
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. Vega is a “repository for high-quality gene models produced by the manual annotation of vertebrate genomes” hosted by the Wellcome Trust Sanger Institute. The Havana group provides manual annotations that clarify the structure and placement of genomic elements for a variety of vertebrate species including ratmouse and human.

To view a sample region, click here. To review the list of most recently annotated rat genes, click here.

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