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.
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. For more information, see 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.
The browser display and database storage of the chains were made by Robert Baertsch and Jim Kent.
Human-Mouse Alignments with BLASTZ. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, and Miller W. Genome Research 2003 Jan;13(1):103-7.
Scoring pairwise genomic sequence alignments. Chiaromonte F, Yap VB, Miller W. Pac Symp Biocomput 2002;:115-26.