QTL Analysis Tools:

• Genome Annotation Tool allows the user to input chromosomal location by base pairs or markers and retrieve a file of ESTs, STS, genes, mRNAs from the region with position, Unigene IDs, homolog information with direct links to NCBI.
• QTL Matchmaker allows the user to determine if sequences of interest lie within QTL regions in a single species or across species.
  - single species
  - cross species

 

Genome Browsers:

• Rat Genome Browser In addition to the typical sequence tracks, RGD’s Genome Browser provides QTL tracks and biological tracks for diseases, phenotypes, pathways, gene function, biological process and cellular component.
• Human Genome Browser RGD also provides a human genome browser with QTL, disease, pathway, phenotype, biological process and cellular component tracks.
• GViewer Gviewer provides users with complete genome view of gene and QTL annotated to a function, biological process, cellular component, phenotype, disease, or pathway.
• UCSC Browser
• Ensembl Browser
• NCBI Browser

GO Analysis Tools:

• GOMiner GoMiner leverages the Gene Ontology to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research.
• Onto-Express , Onto-Compare , Onto-Design ,  Onto-Translate OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. Additional tools are provided for microarray data storing and analysis.

 

Other Tools:

• Genes2Diseases is a database of candidate genes for mapped inherited human diseases. The database is generated using an analysis of relations between phenotypic features and chemical objects, and from chemical objects to Gene Ontology protein function terms, based on the whole MEDLINE and RefSeq databases. Can be used to view all GO terms associated with a particular genetically inherited disease.