## Description

This track shows the best human/$organism chain for every part of the $organism genome. It is useful for finding orthologous regions and for studying genome rearrangement. In full mode the top level (level 1) chains are the largest, highest scoring chains that span this region. In many cases there are gaps in the top level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. The human sequence used in this annotation is from the April 2003 (hg15) assembly.

In the graphical display, the boxes represent ungapped alignments, while the lines represent gaps. Clicking on a box brings up detailed information about the chain as a whole, while clicking on a line brings up information on the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement.

## Methods

First, chains are derived from blastz alignments as described in the details pages of the chain tracks and sorted so that the highest scoring chain in the genome is first. The program chainNet then places chains one at a time, trimming them as necessary to fit into section that is not already covered by a higher scoring chain. During this process, a natural hierarchy emerges where chains that fill gaps in a previous chain are considered underneath the previous chain. The program netSyntenic fills in information about the relationship between upper and lower level chains, including whether a lower level chain is syntenic with the higher level chain, whether it is inverted with respect to the higher level chain, and so forth. The program netClass then fills in how much of the gaps and chains are filled with N's (sequencing gaps) in one or both species, how much is filled with transposons inserted before and after human and $organism diverged, and so forth.

## Credits

The chainNet, netSyntenic, and netClass 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.

Lineage-specific repeats were identified by Arian Smit and his program RepeatMasker.

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