This track shows the best rat/$organism chain for every part of the $organism genome. It is useful for finding orthologous regions and for studying genome rearrangement. The rat sequence used in this annotation is from the Jan. 2003 (rn2) 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.
Chains were derived from blastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.
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 Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.
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.
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).