Mouse Ancestry Mapper Help
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.
Main Display
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; areas in black do not map to any of the ancestral strains. Sequence coordinates are provided at the bottom of the display.
Chromosomal Location
The current chromosome and sequence position is shown in the text box at the top of the display.
To change the current location, enter the sequence location in the format "chr<#>:
Ancestor Coloring
You can change the mapping of ancestral strains to colors by selecting the appropriate strain from each list. Note that each list is filtered by those before it; always select colors from left (yellow) to right (blue).
Navigation
Clicking on the main ancestry display will center and zoom on your position by default.
You can also zoom in or out by clicking on the zoom bar. You can scroll by clicking on the arrow bar on either
side of the viewer.
Pairwise Similarity Measurement
The pairwise similarity between all four ancestral mouse strains for the currently displayed region is shown in the top graph. Each of the six possible pairwise combinations is shown in a different color.
Other Commands
The top button redraws the display with similarities to only three strains (WSB/EiJ, PWD/PhJ, and CAST/EiJ).
The middle button replaces the strict block positions with a the probability that a sequence matches each of the four ancestral HMMs.
The bottom button shows genes, transcripts, ESTs, and other information from the UCSC site.