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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 OntoMate – Ontology-based Literature Search
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.

Rat Bonobo Chinchilla
Mouse Dog Pig
Human Squirrel

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.
InterViewer – Protein-Protein Interactions OLGA – Object List Generator & Analyzer
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. 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.
MOET – Multi-Ontology Enrichment Tool GOLF – Gene and Ortholog Location Finder
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. For a list of genes, find the orthologs in another species, and retrieve the genomic positions of the genes in both species.
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. 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.
Gene Annotator Genome Viewer
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. 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.
RatMine Overgo Probe Designer
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. 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 ACP Haplotyper
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. 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

Additional Tools Available Outside RGD (External Links)
NCBI BLAST VCMap
BLAST uses a heuristic algorithm to detect relationships among sequences which share regions of similarity. The Virtual Comparative Map (VCMap) is a tool for exploring conserved synteny between species, including rat, mouse, human, cow, pig and chicken.
(Runs as a stand-alone Java applet.)
UCSC BLAT Repeat Masker.org
Use BLAT as an alignment tool to map submitted sequence to the genome, and annotate this region in visualization tools. 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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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.