Mouse Diversity Genotyping Array is the most advanced high-density mouse genotyping microarray available. It was designed by Center investigators Drs. Fernando Pardo-Manuel de Villena and Gary Churchill. This single, custom Affymetrix array can simultaneously assay over 600,000 single nucleotide polymorphisms (SNPs) and over 900,000 invariant genomic probes (IGPs) in a mouse DNA sample. The Jackson Laboratory now offers a new Mouse Diversity Genotyping Array Service utilizing this innovative genotyping microarray.

Generic Genome Browser (GBrowse) has been employed to connect datasets produced by Center projects to locations within the mouse genome. In addition to the genomic location, information about the genes and single nucleotide polymorphisms (SNPs) that are present in the same area is also provided. Data currently displayed in the Center’s GBrowse include imputed ancestry from the analysis of 12 strains of mice, along with the phylogenetic trees produced for those regions. Additional data can be added to the Center’s GBrowse database and be displayed alongside the existing content.

Mouse Map Converter is a simple web interface for converting mouse genome coordinates between MIT Markers, Base Pair Positions and Centimorgan Positions. The conversion process is based on the newly calculated mouse map described in "A New Standard Genetic Map for the Laboratory Mouse" by Cox et al.

UNC Computational Genetics Tools were developed by the systems genetics research team at UNC-Chapel Hill for the analysis and visualization of systems biology data.

 

SNP Database – CGDSNP is a high quality single nucleotide polymorphism (SNP) database with more than 8 Million SNPs from 74 strains of laboratory mice, drawn from several sources. These SNPs have been quality checked and curated, integrating SNP data with nearby gene annotations and various functional characteristics and implications of the SNPs, such as amino acid changes, base-pair substitution types, and location within CpG dinucleotides. CGDSNP is accessible online via a web-based query tool. CGDSNP also serves as the interface tool to a recently developed “imputed SNP resource,” in which a Hidden Markov Model (HMM) was used to assess local haplotypes and the most probable base assignment at several million genomic loci in several tens of strains of mice. The imputed SNP calls maybe searched, retrieved, and analyzed identically to the experimentally verified SNPs, with the additional information, such as HMM likelihood score provided in the query return.

Genome Interval Overlap Calculator is a general purpose application for calculating the interval-by-interval overlap between two input files. One use of this application is to use the output from the MouseIBS tool to "filter out" regions of the genome that are identical between two strains. This could be applied to QTLs, gene lists etc.

Mouse Strain Comparison allows you to build strain comparison expressions which are evaluated against the selected strain genomes. This can be used to determine where strains are Identical By State or where strains with a high phenotype differ from strains with a low phenotype etc. For more a more detailed description see the help page.

Researchers within the Churchill Group have developed several software tools for systems level analyses.