Description

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. The $o_organism sequence used in this annotation is from the $o_date ($o_db) assembly.

Display Conventions and Configuration

In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist 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.

In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about 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):

Methods

Chains were derived from blastz alignments using the methods described on the chain tracks description pages. The chains were sorted with the highest-scoring chains in the genome first. The program chainNet was 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 upper and lower level chains, including whether a lower level chain was syntenic with the higher level chain, whether it was inverted with respect to the higher level chain, and so forth. 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, how much was filled with transposons inserted before and after the two organisms diverged, and so on.

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 Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.

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).