Please note, the color scheme on the chainNet tracks to the two
human sequences HG002 paternal and maternal are currently
not colored correctly. We are working on a fix to this issue.
The color scheme for the chainNet tracks to the human sequences
GRCh37/hg19 and GRCh38/hg38 are colored correctly.
This track shows regions of this target genome (T2T-CHM13v2.0 - 2022-01-24) that has alignment
to other query 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.
Other query genome assemblies aligning to this target genome assembly:
Each of the query genome alignments are represented in this display
with four types of summaries, with two tracks for each type: a chain/net set.
- complete pair-wise alignment before any filtering
- syntenic net, the full alignment filtered for syntenic alignments only
- reciprocal best, the full alignment filtered for reciprocal best alignments only
- lift over, the full alignment filtered for the best target/query alignments only
The chain tracks shows alignments of the other genome assemblies to the
T2T-CHM13v2.0/GCA_009914755.4/2022-01-24 genome using a gap scoring system that allows longer gaps
than traditional affine gap scoring systems. It can also tolerate gaps in both
query and target geomes 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
query assembly or an insertion in the target
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 target 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 alignment of the best query/target chain for
every part of the target genome. It is useful for
finding syntenic regions, possibly orthologs, and for studying genome
command line program: chainNet is used to convert
a chain alignment to the net representation of that alignment. This is
a filter that eliminates low quality chains and accumulates chains in
synteny together into one net representating that synteny block.
Display Conventions and Configuration
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 query as it aligned to target. When the view is
too large to show such detail, a graph of the alignment score will be
The query genome was aligned to target 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 query chromosome and a single
target 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
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
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.
(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.
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
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