Description

This track shows best-in-genome chimpanzee/human alignments based on the chimpanzee/human alignment net; i.e., the best chain for every part of the human genome. This track displays alignment scores, and when zoomed in to the base level, the alignment itself is displayed. The human sequence used in this annotation is from the July 2003 (hg16) assembly.

In the graphical display, the shade (in dense display mode) or height (in full mode) of a vertical line indicates the score of the best chained and netted alignment at that location. Clicking on the track brings up detailed information about the alignments in the currently displayed range of positions.

Methods

First, chains are derived from blastz and blat alignments as described in the description page of the Human Chain track. Subsequently, these chains were merged, sorted, and netted to obtain the best alignments. These methods are described in the Human Net track description.

Credits

The chaining and netting programs were developed at the University of California at Santa Cruz by Jim Kent. For more information, see Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D (2003). Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20):11484-11489 Sep 30 2003.