Description

This tracks shows rat/$organism genomic alignments using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rat and $organism simultaniously. These 'double-sided' gaps can be caused by local inversions, and overlapping deletions in both species.

Methods

Transposons that have been inserted since the rat/$organism split are removed, and the resulting abbreviated genomes are aligned with blastz. The transposons are then put back into the alignments. The resulting alignments are converted into axt format and the resulting axts are fed into axtChain. AxtChain organizes all the alignments between a single rat and a single $organism 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 displayed here.

Credits

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

The browser display and database storage of the chains were made by Robert Baertch and Jim Kent.