Description

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. This track displays alignment scores, and when zoomed in to the base level, the alignment itself is displayed. The $o_organism sequence is from WormBase Version cb25.agp8 ($o_date ) assembly.

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.

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 $organism and $o_organism diverged, and so forth. The program netToAxt translates the net back to axt. netToAxt is run with -maxGap=300.

Credits

The chainNet, netSyntenic, netClass and netToAxt 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.