Mouse Haplotype Analysis
The sequences of 16 commonly used, genetically diverse strains of inbred laboratory mice were analyzed to determine their haplotype structure. The Ancestry Browser shows which ancestral sequence each inbred strain most resembles, along with statistics on the pairwise similarity between the ancestral strains. The Haplotype Viewer shows the haplotype block boundaries and the pairwise similarity for all 56 strains: the 15 used for SNP discovery, the reference strain (C57BL/6J), and the 40 additional strains for which the genotypes were imputed.
More details can be found in Frazer (2007) [1].
Mouse Ancestry Mapper
The origins of the 12 classical inbred strains were mapped against the four ancestral wild derived strains. Hidden Markov models (HMMs) were trained to recognize the variants in the WSB/EiJ (domesticus), PWD/PhJ (musculus), CAST/EiJ (castaneus), and MOLF/EiJ (molossinus) strains. Each variant in the inbred strains was then scored against the ancestral HMMs; positions in the inbred strains are classified by the wild strain they best match.
Sequence block boundaries are defined where an inbred strain's ancestry switches from one ancestor to another. The color represents the strain's closest ancestor; areas that are grey lack enough information to make a prediction. For more details, see the documentation.
Mouse Haplotype Block Viewer
Haplotype blocks of 16 inbred mouse strains (including wild-derived strains) were predicted by merging the results of pairwise comparisons of the mouse strains. The pairwise scores were determined by using a HMM trained to detect low-SNP-density and high-SNP-density regions. Haplotype block regions are detected when the matching HMM changes state from low-density to high-density or vice-versa. The 40 additional strains, for which genotypes of the 8.27 million SNPs were imputed, are also included in this haplotype block viewer.
In the visualization, a haplotype block will be colored either with a preceeding strain's color if it matches, or with its own strain color otherwise. For more details, see the documentation.
[1] Frazer, K.A. et al. Nature. 2007 A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448, 1050-3 (2007).