## Description

This track displays multiz alignments of three Drosophila species:

- $Organism ($date, $db)
- D. yakuba (Apr. 2004, droYak1)
- D. pseudoobscura (Aug. 2003, dp1)

## Methods

Blastz was used to create pairwise alignments to $Organism of D. yakuba and of D. pseudoobscura. Alignments were chained (axtChain) and netted (chainNet, netSyntenic, netClass). Then single-coverage/best-in-genome sets of pairwise alignments were extracted from the nets. These pairwise alignments were processed into multiple alignments by multiz.

## Credits

This track was created at UCSC using the Multiz program created by Minmei Hou and Webb Miller of the Penn State Bioinformatics Group. Jim Kent wrote the axtChain, chainNet, netSyntenic and netClass programs.

## References

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. (2004). Aligning Multiple Genomic Sequences with the Threaded Blockset Aligner. Genome Res. 14(4):708-15.

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.

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002;:115-26.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, and Miller W. (2003). Human-Mouse Alignments with BLASTZ. Genome Res. 13(1):103-7.