Description
Theses chain track shows alignments of human ($db) to GRCh38 to
other genomes using a gap scoring system that allows longer gaps
than traditional affine gap scoring systems. It can also tolerate gaps in both
human and the other genome 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
human assembly or an insertion in the other 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 other 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.
Methods
Transposons that have been inserted since the human/other
split were removed from the assemblies. The abbreviated genomes were
aligned with lastz, and the transposons were added back in.
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 human chromosome and a single
chromosome from the other genome 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.
$matrix
Chains scoring below a minimum score of '$chainMinScore' were discarded;
the remaining chains are displayed in this track. The linear gap
matrix used with axtChain:
$chainLinearGap
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.
Data access
Release history
- 2020-10-21 t2t-chm13-v1 assembly
- 2020-08-12 t2tChm13_20200727 assembly
Contacts
Credits
Chain/Net:
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
Lastz:
Harris RS.
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis. Pennsylvania State University, USA. 2007.
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
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