## 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. The human sequence used in this annotation is from the July 2003 (hg16) assembly.

## Display Conventions and Configuration

The track displays alignment scores and, when zoomed in to the base level, the alignment itself. In the graphical display, the shade (in dense display mode) or height (in full display mode) of a vertical line indicates the score of the best chained and netted alignment at that location. Click on the track to view detailed information about the alignments in the currently displayed range of positions.

## Methods

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

## Credits

The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent.

Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.

The browser display and database storage of the nets were made by Robert Baertsch and Jim Kent.

## References

Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-Mouse Alignments with BLASTZ. Genome Res. 13(1), 103-7 (2003).