Description
Chain Track
The chain track shows alignments of human (Dec. 2013 (GRCh38/hg38)) 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
other assembly or an insertion in the human 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.
Net Track
The net track shows the best human/other chain for
every part of the other genome. It is useful for
finding orthologous regions and for studying genome
rearrangement. The human sequence used in this annotation is from
the Dec. 2013 (GRCh38/hg38) assembly.
Display Conventions and Configuration
Chain Track
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.
Net Track
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):
- Top - the best, longest match. Displayed on level 1.
- Syn - line-ups on the same chromosome as the gap in the level above
it.
- Inv - a line-up on the same chromosome as the gap above it, but in
the opposite orientation.
- NonSyn - a match to a chromosome different from the gap in the
level above.
Methods
Chain track
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.
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The following lastz matrix was used
for the alignments to: Wallaby, Tasmanian Devil
| | A | C | G | T |
| A | 91 | -114 | -31 | -123 |
| C | -114 | 100 | -125 | -31 |
| G | -31 | -125 | 100 | -114 |
| T | -123 | -31 | -114 | 91 |
| |
The following lastz matrix was used
for the alignments to: American Alligator, Medium Ground Finch,
Opossum, Platypus, Chicken, Zebra Finch, Lizard, X. tropicalis,
Stickleback, Fugu, Zebrafish, Tetraodon, Medaka, Lamprey
| | A | C | G | T |
| A | 91 | -90 | -25 | -100 |
| C | -90 | 100 | -100 | -25 |
| G | -25 | -100 | 100 | -90 |
| T | -100 | -25 | -90 | 91 |
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For the Wallaby alignment, chains scoring below a minimum score
of '3000' were discarded; the remaining chains are displayed in this track.
The linear gap matrix used with axtChain:
-linearGap=medium
tableSize 11
smallSize 111
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300
For the alignments to: American Alligator, Medium Ground Finch, Tasmanian Devil, Opossum, Platypus, Chicken,
Zebra Finch, Lizard, X. tropicalis, Stickleback, Fugu, Zebrafish, Tetraodon,
Medaka and Lamprey, chains scoring below a minimum score
of '5000' were discarded; the remaining chains are displayed
in this track. The linear gap matrix used with axtChain:
-linearGap=loose
tablesize 11
smallSize 111
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
See also: lastz parameters used in these alignments,
and chain minimum score and gap parameters used in these alignments.
Net track
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.
Credits
LASTZ was developed at
Miller Lab at Pennsylvania State University by
Bob Harris.
Lineage-specific repeats were identified by Arian Smit and his
RepeatMasker
program.
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.
References
Harris RS.
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis. Pennsylvania State University, USA. 2007.
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
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