This track shows the best mouse/cow chain for
every part of the cow genome. It is useful for
finding orthologous regions and for studying genome
rearrangement. The mouse sequence used in this annotation is from
the July 2007 (mm9) assembly.
Display Conventions and Configuration
In full display mode, the top-level (level 1)
chains are the largest, highest-scoring chains that
span this region. In many cases gaps exist in the
top-level chain. When possible, these are filled in by
other chains that are displayed at level 2. The gaps in
level 2 chains may be filled by level 3 chains and so
In the graphical display, the boxes represent ungapped
alignments; the lines represent gaps. Click
on a box to view detailed information about the chain
as a whole; click on a line to display information
about the gap. The detailed information is useful in determining
the cause of the gap or, for lower level chains, the genomic
Individual items in the display are categorized as one of four types
(other than gap):
Top - the best, longest match. Displayed on level 1.
Syn - line-ups on the same chromosome as the gap in the level above
Inv - a line-up on the same chromosome as the gap above it, but in
the opposite orientation.
NonSyn - a match to a chromosome different from the gap in the
Chains were derived from blastz alignments, using the methods
described on the chain tracks description pages, and sorted with the
highest-scoring chains in the genome ranked first. The program
chainNet was then used to place the chains one at a time, trimming them as
necessary to fit into sections not already covered by a higher-scoring chain.
During this process, a natural hierarchy emerged in which a chain that filled
a gap in a higher-scoring chain was placed underneath that chain. The program
netSyntenic was used to fill in information about the relationship between
higher- and lower-level chains, such as whether a lower-level
chain was syntenic or inverted relative to the higher-level chain.
The program netClass was then used to fill in how much of the gaps and chains
contained Ns (sequencing gaps) in one or both species and how much
was filled with transposons inserted before and after the two organisms
The chainNet, netSyntenic, and netClass programs were
developed at the University of California
Santa Cruz by Jim Kent.
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 program
The browser display and database storage of the nets were made
by Robert Baertsch and Jim Kent.