Description

This track shows the $o_organism/$organism alignment net for every part of the $organism genome. It is useful for finding orthologous regions and for studying genome rearrangement. The $o_organism sequence used in this annotation is from the $o_date ($o_db) assembly.

In the graphical display, the boxes represent ungapped alignments, while the lines represent gaps. 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 chains. When possible, these are filled in by other chains displayed at Level 2. The gaps in Level 2 chains may be filled by Level 3 chains and so forth. Clicking on a box displays detailed information about the chain as a whole, while clicking on a line shows information on the gap. The detailed information is useful in determining the cause of the gap or, for lower-level chains, the genomic rearrangement.

Individual track features are categorized as one of four types (other than gap):

Methods

These alignments were generated using blastz and blat alignments of genomic sequence from the $o_date $o_organism genome assembly (UCSC $o_db, NCBI Build 34). The initial alignments were generated using blastz on repeatmasked sequence using the following $organism/$o_organism scoring matrix:

     A    C    G    T
A   100 -300 -150 -300
C  -300  100 -300 -150
G  -150 -300  100 -300
T  -300 -150 -300  100

K = 4500, L = 3000,  Y = 3400, H = 2000

The resulting alignments were processed by the axtChain program. AxtChain organizes all the alignments between a single $organism scaffold and a single $o_organism chromosome into a group and makes a kd-tree out of all the gapless subsections (blocks) of the alignments. The maximally-scoring chains of these blocks were found by running a dynamic program over the kd-tree. Chains scoring below a certain threshold were discarded.

To place additional $organism scaffolds that were not initially aligned by blastz, a DNA blat of the unmasked sequence was performed. The resulting blat alignments were also chained, and then merged with the blastz-based chains produced in the previous step to produce a merged set of chains, which are displayed in the "Human Chain" track.

These chains were sorted such that the highest scoring chain in the genome was first. The program chainNet was then used to place each chain one at a time, trimming it as necessary to fit into a section not already covered by a higher-scoring chain. During this process, a natural hierarchy emerges in which chains that fill gaps in a previous chain are considered underneath the previous chain. The program netSyntenic was used to fill 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.

Credits

The chaining and netting 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.

The browser display and database storage of the nets were made by Robert Baertsch and Jim Kent.