Description

This track shows $o_organism/$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 organisms 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 genome of the non-$organism species 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 $o_organism/$organism split were removed, and the resulting abbreviated genomes were aligned using blastz. The transposons were then put back into the alignments. The resulting alignments were converted into axt format and the resulting axts fed into axtChain. This program organizes all the alignments between a single $o_organism 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 in this track.

Lineage-specific repeats were not used for these alignments.

Credits

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 browser display and database storage of the chains were made by Rachel Harte and Jim Kent.

References

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

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