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RGD Tools

In addition to the collection and storage of data, RGD provides a variety of information 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, the second list is of external tools of high relevance to RGD users.

 
RGD Tools

 

Tool Name Brief description of functionality
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
BLAST Uses a heuristic algorithm to detect relationships among sequences which share regions of similarity
BLAT An alignment tool to map submitted sequence to the genome, and annotate this region in visualization tools
Genome Annotation 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
Genome Scanner
 Assists 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
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
Human Genome Browser Using a sequence name, gene name, locus, oligonucleotide (15 bp minimum) or other landmark you can search for its location on the human genome
Metagene
 Provides 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
Rat Genome Browser Using a sequence name, gene name, locus, oligonucleotide (15 bp minimum) or other landmark you can search for its location on the rat genome
Repeat Masker 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
RH MapServer
 Allows users to place their own radiation hybrid vectors against the MCW RH framework map
Search Tools
 Provide text/keyword search access to RGD
VCMap Comparative mapping tool, allows the prediction of syntenic regions between the rat, mouse and human genomes

 
External Tools

The following tools are available at other sites and provide complementary functionality to those available at RGD. If there are other tools we have omitted, please contact us so we may include them.

BLAST tools and other sequence comparison methods
NCBI BLAST (all sequences)
NCBI Rat Blast (Rat genomic sequence)
Baylor Rat Blast (Blast against the Genome Sequencing consortiums dataset of BACs and whole genome shotgun data)
MGI Rodent Blast (Blast against mouse and rat sequences)
UCSC Blat (use to align rat sequences against human and mouse genomic sequences)
Pipmaker (use to provide a graphical alignment of two genomic sequences)
Mapping tools
Rat RH Mapping server @ U. Tokyo
Ratmap Gene And Position Predictor (GAPP)
 

 

 

 


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