## Description

This track shows blastz scores from the D. pseudoobscura/D. melanogaster Alignment Net track, i.e. the best D. pseudoobscura/D. melanogaster chain for every part of the D. pseudoobscura genome. The D. melanogaster sequence is from the Berkeley Drosophila Genome Project Release 3.1 (Jan. 2003) assembly.

## Display Conventions and Configuration

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

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 translated the net back to axt, using the setting -maxGap=300.

## Credits

The chainNet, netSyntenic, netClass and netToAxt 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.

The browser display and database storage of the nets were made by Robert Baertsch and Jim Kent.

## 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).