This track shows best-in-genome $organism/$o_organism alignments based on the $organism/$o_organism alignment net, i.e. the best chain for every part of the $organism genome. The $o_organism sequence is from WormBase Version cb25.agp8 ($o_date ) assembly.
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 mode) of a vertical line indicates the score of the best chained and netted alignment at that location. Clicking on the track brings up detailed information about the blastz alignments (taken from the axt-formatted output) in the currently displayed range of positions.
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 program netToAxt translates the net back to axt. netToAxt is run with -maxGap=300.
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.
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).