Description
This tracks 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 $organism simultaniously. These 'double-sided'
gaps can be caused by local inversions, and overlapping deletions
in both species.
Methods
Transposons that have been inserted since the mouse/$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 Baertch and Jim Kent.