Genome Tools

RGD provides a variety of tools to search and analyze both thedata 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.

    Rat Genome Browsers

    Gene Annotator

Genome browsers allow the user to view objects such as genes, variants, QTLs, and so forth in their genomic context.  RGD currently supports two genome browsers. Click here for help getting started with RGD's browsers or click one of these links to select your browser of choice:

 

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.

 

    Human Genome Browsers

    Genome Viewer

Genome browsers allow the user to view objects such as genes, variants, QTLs, and so forth in their genomic context.  RGD currently supports two genome browsers.  Click here for help getting started with RGD's browsers or click one of these links to select your browser of choice:

 

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.

 

   Mouse Genome Browsers

    Variant Visualizer

Genome browsers allow the user to view objects such as genes, variants, QTLs, and so forth in their genomic context.  RGD currently supports two genome browsers.  Click here for help getting started with RGD's browsers or click one of these links to select your browser of choice:

 

Variant Visualizer is a viewing and analysis tool for sequence polymorphisms.  The data currently contain 26 rat strains sequenced by 4 independent institutions. Select strains 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 SNPs which match the input criteria, including in many cases information on read depth, zygosity, conservation score and more.

 

    Overgo Probe Designer   

   SNPlotyper

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.

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.

 

  ACP Haplotyper

     RatMine      

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

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.

 

   Genome Scanner


  VCMap

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 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.

Additional Tools Available Outside RGD (External Links)

  NCBI BLAST

  UCSC BLAT

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 Masker.org

  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 rat, mouse and human.

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

Tool Archive (No Longer Available)

  MetaGene

    BioMart 

The MetaGene tool has been retired and removed from the RGD website (as of December 15th, 2009)

 Click here for more information and possible alternatives.

RGD and the MCW Proteomics Center have retired the MCW BioMart tool (effective May 20th, 2011).  This tool is NO LONGER AVAILABLE.  Click here to learn more.

Click here to go directly to RatMine.