This track shows the best $o_organism/$organism chain 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 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 forth.
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 rearrangement.
Individual items in the display are categorized as one of four types (other than gap):
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 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 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 Ross Hardison.
The browser display and database storage of the nets were made by Robert Baertsch and Jim Kent.
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-Mouse Alignments with BLASTZ. Genome Res. 13(1), 103-7 (2003).