## Description

This track 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 simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.

The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the $o_organism assembly or an insertion in the $organism assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where there are multiple chains over a particular portion of the $organism genome, chains with single-lined gaps often are due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and non-prodessed pseudogenes.

## Methods

Transposons that have been inserted since the rat/$organism split were removed, and the resulting abbreviated genomes were aligned with blastz. The transposons were then put back into the alignments. The resulting alignments were converted into axt format and the resulting axts were fed into axtChain. AxtChain organizes all the alignments between a single rat and a single $organism chromosome into a group and creates a kd-tree out of all the gapless subsections (blocks) of the alignments. Next, maximally scoring chains of these blocks were found by running a dynamic program over the kd-tree. Chains scoring below a threshold were discarded; the remaining chains are displayed here.

## Credits

Blastz was developed at Pennsylvania State University by Minmei Hou, 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 generated by Robert Baertsch and Jim Kent.

## References

Chiaromonte, F., Yap, V.B., Miller, W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002, 115-26 (2002).

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).