## Description

This track shows D. melanogaster protein-coding genes annotated by the Berkeley Drosophila Genome Project (BDGP). The gene locations have been mapped onto the D. pseudoobscura sequence using chained whole-genome D. pseudoobscura/D. melanogaster blastz alignments.

## Methods

For a description of the methods used to generate the data shown in this track, see the BDGP Methods web page.

The genomes of D. pseudoobscura and D. melanogaster are aligned with blastz. The resulting alignments are converted into axt format and the resulting axts are fed into axtChain. AxtChain organizes all the alignments between a single D. pseudoobscura scaffold and a single D. melanogaster chromosome into a group, and makes a kd-tree out of all the gapless subsections (blocks) of the alignments. Next, maximally scoring chains of these blocks are found by running a dynamic program over the kd-tree. Chains scoring below a threshold are discarded, and the remaining chains are used by the liftOver program to translate D. melanogaster coordinates into D. pseudoobscura coordinates for display in this track. Because of the evolutionary distance between the two species and the incomplete sequence of D. pseudoobscura, liftOver was run with relaxed constraints (minimum 50% matching bases, minimum 50% mapping of aligned blocks/exons, tolerate missing start/end of CDS).

## Credits

Thanks to the Berkelely Drosophila Genome Project for providing these data.

Blastz was developed at Pennsylvania State University by Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.

The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.

The liftOver program was developed at the University of California at Santa Cruz by Jim Kent.