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. Click here for video tutorials and click here for the help pages for getting started with RGD’s tools.
Analysis & Visualization
 VCMap – Virtual Comparative Map (beta version)  |
 MOET – Multi-Ontology Enrichment Tool |
| The Virtual Comparative Map (VCMap) is a tool for exploring conserved synteny between species, including rat, mouse and human. | For a list of genes, find the terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over-represented in the annotations for those genes, or for orthologs in other species. Click here for help getting started with RGD’s MOET. |
 PhenoMiner – Quantitative Phenotypes  |
 JBrowse – Genome Browsers |
| 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. Click here for help getting started with RGD’s PhenoMiner. | View genes, transcripts, variants, QTLs, etc in their genomic context. RGD has genome browsers for all of the species and assemblies for which we have data. Click here for help getting started with RGD’s browsers. |
 Variant Visualizer |
 OLGA – Object List Generator & Analyzer |
| For a genomic region or list of genes and one or more samples of interest, view and analyze rat strain-specific sequence polymorphisms and human variants from ClinVar. Filter results based on parameters such as variant consequences (damaging vs. benign), clinical significance, sequence type and call statistics. | Enter a list of genes, QTLs or strains, or create new lists based on genomic position and/or functional annotations. Flexibly combine your lists, then send the final result to other RGD tools for analysis. |
 GViewer – Genome Viewer |
 InterViewer – Protein-Protein Interactions |
| GViewer searches for matching terms from any or all of the ontologies in use for curation at RGD and provides a genome-wide view of the genes, QTLs and/or strains annotated to those terms. Click here for help getting started with GViewer. | For a list of rat, mouse, dog and/or human genes or proteins, this Cytoscape-based interaction viewer will display pairwise protein interactions, with corresponding links to gene records in RGD and the originating interaction records at IMEX. |
 GA Tool – Gene Annotator |
 GOLF – Gene and Ortholog Location Finder |
| For a list of gene symbols or IDs, or a chromosomal region, retrieve all functional annotations for the genes and their orthologs, as well as links to additional information at other databases. | For a list of genes, find the orthologs in another species, and retrieve the genomic positions of the genes in both species. |
Literature Search |
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| OntoMate is an ontology-driven, concept-based literature search engine developed as an alternative for the basic PubMed search engine. All abstracts in PubMed have been tagged with gene symbols/names and ontology terms to facilitate retrieval of the most relevant results. | |
