Description
This track shows best-in-genome
$organism/$o_organism alignments based on the
$organism/$o_organism alignment net; i.e., the best chain
for every part of the $organism genome. This track displays alignment
scores, and when zoomed in to the base level, the alignment itself is displayed.
The $o_organism sequence is from
WormBase
Version cb25.agp8 ($o_date ) assembly.
In the graphical display, the shade (in dense display mode)
or height (in full mode) of a vertical line indicates the score
of the best chained and netted alignment at that location.
Clicking on the track brings up detailed information about the
blastz alignments (taken from the axt-formatted output) in the
currently displayed range of positions.
Methods
First, chains are derived from
blastz
alignments as described in the details pages of the chain tracks
and sorted so that the highest scoring chain in the
genome is first. The program chainNet then places
chains one at a time, trimming them as necessary to
fit into section that is not already covered by
a higher scoring chain. During this process, a
natural hierarchy emerges where chains that fill gaps
in a previous chain are considered underneath the
previous chain. The program netSyntenic fills in
information about the relationship between upper
and lower level chains, including whether a lower level
chain is syntenic with the higher level chain, whether
it is inverted with respect to the higher level chain,
and so forth. The program netClass then fills in
how much of the gaps and chains are filled with N's
(sequencing gaps) in one or both species, how much
is filled with transposons inserted before and after
$organism and $o_organism diverged, and so forth.
The program netToAxt translates the net back
to axt. netToAxt is run with -maxGap=300.
Credits
The chainNet, netSyntenic, netClass and netToAxt programs were
developed at the University of California
at Santa Cruz by Jim Kent.
For more information, see
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.
Lineage-specific repeats were identified by Arian Smit and his
program RepeatMasker.