This track shows alignments of the $organism genome with itself, using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. The system can also tolerate gaps in both sets of sequence simultaneously. After filtering out the "trivial" alignments produced when identical locations of the genome map to one another (e.g. chr22 maps to chr22), the remaining alignments point out areas of duplication within the $organism genome.
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 query assembly or an insertion in the target assembly. Double lines represent more complex gaps that involve substantial sequence in both assemblies. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one of the assemblies. In cases where there are multiple chains over a particular portion of the $organism genome, chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.
The display indicates the chromosome, strand, and location of the match for each matching alignment (in thousands).
The genome is aligned to itself using blastz. Trivial alignments are filtered out. The remaining alignments are converted into axt format and the resulting axts are fed into axtChain. AxtChain organizes all the alignments between a single target and a single query 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.
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 Hiram Clawson (hiram@soe.ucsc.edu) and Jim Kent.
Chiaromonte F, Yap VB, Miller W (2002). Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002;:115-26.
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.
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, and Miller W (2003). Human-Mouse Alignments with BLASTZ. Genome Res. 13(1):103-7.