This track shows the best $o_organism/$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 $o_date/$o_db $o_organism assembly was used for these aligments.
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.
Individual items in the display are categorized as one of four types (other than gap):
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.