Description

This track shows Mouse/$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 mouse and $organism simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The mouse sequence is from the Oct. 2003 (mm4) assembly.

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 missing sequence in the non-$organism species. Double lines represent gaps in the chain where sequence is present in both species but they do not align. 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. In the fuller display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.

Methods

Transposons that have been inserted since the mouse/$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 mouse 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 Baertsch and Jim Kent.

References

Human-Mouse Alignments with BLASTZ. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler H, 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.