This track shows alignments of mouse (mm9, July 2007) to the
cow genome using a gap scoring system that allows longer gaps
than traditional affine gap scoring systems. It can also tolerate gaps in both
mouse and cow 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
mouse assembly or an insertion in the cow
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 multiple chains align over a particular region of
the cow genome, the 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 "pack" and "full" display
modes, the individual feature names indicate the chromosome, strand, and
location (in thousands) of the match for each matching alignment.
Display Conventions and Configuration
By default, the chains to chromosome-based assemblies are colored
based on which chromosome they map to in the aligning organism. To turn
off the coloring, check the "off" button next to: Color
track based on chromosome.
To display only the chains of one chromosome in the aligning
organism, enter the name of that chromosome (e.g. chr4) in box next to:
Filter by chromosome.
Transposons that have been inserted since the mouse/cow
split were removed from the assemblies. The abbreviated genomes were
aligned with blastz, and the transposons were added back in.
The resulting alignments were converted into psl format using the lavToPsl
program. The psl alignments were fed into axtChain, which organizes all
alignments between a single mouse chromosome and a single
cow chromosome into a group and creates a kd-tree out
of the gapless subsections (blocks) of the alignments. A dynamic program
was then run over the kd-trees to find the maximally scoring chains of these
The following matrix was used:
Chains scoring below a threshold were discarded; the remaining
chains are displayed in this track.
Blastz was developed at Pennsylvania State University by
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from
Lineage-specific repeats were identified by Arian Smit and his
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 generated
by Robert Baertsch and Jim Kent.