This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns.
The chain track shows alignments of Cow/(Apr. 2018 (ARS-UCD1.2/bosTau9)) to the hybrid cattle/Bos indicus x Bos taurus/GCF_003369695.1/2018-11-30 genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both Cow and hybrid cattle 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 Cow assembly or an insertion in the hybrid cattle 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 hybrid cattle 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.
The net track shows the best Cow/hybrid cattle chain for every part of the hybrid cattle genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The Cow sequence used in this annotation is from the Apr. 2018 (ARS-UCD1.2/bosTau9) assembly.
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.
At base level in full display mode, this track will show the sequence of Cow as it aligned to hybrid cattle. When the view is too large to show such detail, a graph of the alignment score will be shown.
The Cow genome was aligned to hybrid cattle genome with lastz. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single Cow chromosome and a single hybrid cattle 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 blocks.
Chains were derived from lastz 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 diverged.
The resulting net file was converted to axt format via netToAxt, then converted to maf format via axtToMaf, then converted to the bigMaf format with mafToBigMaf and bedToBigBed
lastz was developed by Robert Harris, Pennsylvania State University.
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 and nets were created by Robert Baertsch and Jim Kent.
The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent.
Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University
Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961