Zoonomia+Primates 447:
Another Zoonomia mammalian alignment, built on a different species set
Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
Warning: Unlike other alignment tracks on the genome browser, this one does not show
insertions in the query genomes. Also, all other alignment tracks show one query
genome sequence for each target genome sequence, but in this track, each
target genome sequence can be aligned to multiple query genome sequences.
Only the first sequence is shown on the genome browser itself, the others are shown on the details page,
when one clicks on the alignment. If you are interested in this track and want
these shortcomings to be fixed, please contact us.
This track shows multiple alignments of 241 vertebrate
species and measurements of evolutionary conservation
from the Zoonomia Project.
The multiple alignments were generated using the
Cactus comparative genomics alignment system.
Cactus produces reference-free, whole-genome multiple alignments.
The base-wise conservation scores are computed using phyloP from the
PHAST package, for all species.
This version was prepared by Michael Dong (Uppsala U) with an improved neutral
model incorporating better versions of ancestral repeats.
For genome assemblies not available in the genome browser, there are
alternative assembly hub genome browsers. Missing sequence in any assembly is
highlighted in the track display by regions of yellow when zoomed out and by
Ns when displayed at base level (see Gap Annotation, below).
Table 1.Genome assemblies included in the 241-way Conservation track. Species status:LC = Least Concern; NT = Near threatened; VU = Vulnerable; EN = Endangered; CR = Critically endangered
Display Conventions and Configuration
In full and pack display modes, conservation scores are displayed as a
wiggle track (histogram) in which the height reflects the
size of the score.
The conservation wiggles can be configured in a variety of ways to
highlight different aspects of the displayed information.
Click the Graph configuration help link for an explanation
of the configuration options.
Pairwise alignments of each species to the human genome are
displayed below the conservation histogram as a grayscale density plot (in
pack mode) or as a wiggle (in full mode) that indicates alignment quality.
In dense display mode, conservation is shown in grayscale using
darker values to indicate higher levels of overall conservation
as scored by phastCons.
Checkboxes on the track configuration page allow selection of the
species to include in the pairwise display.
The names of selected species are colored according to their clade,
alternating between blue and green.
Note that excluding species from the pairwise display does not alter the
conservation score display.
To view detailed information about the alignments at a specific
position, zoom the display in to 30,000 or fewer bases, then click on
the alignment.
Gap Annotation
The Display chains between alignments configuration option
enables display of gaps between alignment blocks in the pairwise alignments in
a manner similar to the Chain track display. The following
conventions are used:
Single line: No bases in the aligned species. Possibly due to a
lineage-specific insertion between the aligned blocks in the human genome
or a lineage-specific deletion between the aligned blocks in the aligning
species.
Double line: Aligning species has one or more unalignable bases in
the gap region. Possibly due to excessive evolutionary distance between
species or independent indels in the region between the aligned blocks in both
species.
Pale yellow coloring: Aligning species has Ns in the gap region.
Reflects uncertainty in the relationship between the DNA of both species, due
to lack of sequence in relevant portions of the aligning species.
Genomic Breaks
Discontinuities in the genomic context (chromosome, scaffold or region) of the
aligned DNA in the aligning species are shown as follows:
Vertical blue bar: Represents a discontinuity that persists indefinitely
on either side, e.g. a large region of DNA on either side of the bar
comes from a different chromosome in the aligned species due to a large scale
rearrangement.
Green square brackets: Enclose shorter alignments consisting of DNA from
one genomic context in the aligned species nested inside a larger chain of
alignments from a different genomic context. The alignment within the
brackets may represent a short misalignment, a lineage-specific insertion of a
transposon in the human genome that aligns to a paralogous copy somewhere
else in the aligned species, or other similar occurrence.
Base Level
When zoomed-in to the base-level display, the track shows the base
composition of each alignment. The numbers and symbols on the Gaps
line indicate the lengths of gaps in the human sequence at those
alignment positions relative to the longest non-human sequence.
If there is sufficient space in the display, the size of the gap is shown.
If the space is insufficient and the gap size is a multiple of 3, a
"*" is displayed; other gap sizes are indicated by "+".
Codon translation is available in base-level display mode if the
displayed region is identified as a coding segment. To display this annotation,
select the species for translation from the pull-down menu in the Codon
Translation configuration section at the top of the page. Then, select one of
the following modes:
No codon translation: The gene annotation is not used; the bases are
displayed without translation.
Use default species reading frames for translation: The annotations from
the genome displayed in the Default species to establish reading frame
pull-down menu are used to translate all the aligned species present in the
alignment.
Use reading frames for species if available, otherwise no translation:
Codon translation is performed only for those species where the region is
annotated as protein coding.
Use reading frames for species if available, otherwise use default species:
Codon translation is done on those species that are annotated as being protein
coding over the aligned region using species-specific annotation; the remaining
species are translated using the default species annotation.
Codon translation uses the following gene tracks as the basis for translation:
The Zoonomia alignment was composed of two sets of mammalian genomes: newly
assembled DISCOVAR assemblies and GenBank assemblies. The DISCOVAR genomes
were masked with RepeatMasker (commit 2d947604), using Repbase version
20170127 as the repeat library and CrossMatch as the alignment engine. The
pipeline used is available at
repeatMaskerPipeline
(commit a6ad966). The
guide-tree topology was taken from the TimeTree database (using release
current in October 2018), and the branch lengths were estimated using the
least-squares-fit mode of PHYLIP, version
3.695. The distance matrix used was largely based on distances from the 4d
site trees from the UCSC browser. To add those species not present in the
UCSC tree, approximate distances estimated by Mash (commit 541971b)
to the closest UCSC species
were added to the distance between the two closest UCSC species. We used the
HAL package (commit 68db41d)
produce the HAL file.
Phylogenetic Tree Model
The phyloP are phylogenetic methods that rely
on a tree model containing the tree topology, branch lengths representing
evolutionary distance at neutrally evolving sites, the background distribution
of nucleotides, and a substitution rate matrix.
The
all-species tree model for this track was
generated using the phyloFit program from the PHAST package
(REV model, EM algorithm, medium precision) using multiple alignments of
4-fold degenerate sites extracted from the 241-way alignment
(msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene
set, filtered to select single-coverage long transcripts.
This same tree model was used in the phyloP calculations; however, the
background frequencies were modified to maintain reversibility. The resulting
models are in the
phyloP241way download directory as .mod files: a general
model, plus separate models for chrX and chrY.
PhyloP Conservation
The phyloP program supports several different methods for computing
p-values of conservation or acceleration, for individual nucleotides or
larger elements (
http://compgen.cshl.edu/phast/). Here it was used
to produce separate scores at each base (--wig-scores option), considering
all branches of the phylogeny rather than a particular subtree or lineage
(i.e., the --subtree option was not used). The scores were computed by
performing a likelihood ratio test at each alignment column (--method LRT),
and scores for both conservation and acceleration were produced (--mode
CONACC).
Data Access
The alignments and the conservation scores can be retrieved for a single region or for a list of
regions with the Table Browser,
which returns the alignments in MAF format and the scores as wiggle data. The conservation
scores, though not the alignments, can also be joined with other annotations in the Data Integrator. For automated access, our REST API serves the alignment and conservation tracks
individually, by name.
Downloads for data in this track are available:
Cactus alignments (MAF format), and phylogenetic trees, and PhyloP conservation (WIG and bigWig format)
Genome-wide alignment and conservation files are large. Among our command-line programs,
mafsInRegion, mafSpeciesSubset and mafFrags pull out a region, a
subset of species, or the alignment underlying a gene, and bigWigToWig and
bigWigSummary read the conservation files. They can be downloaded from the utilities directory, and
each one prints its usage when run with no arguments. See our Data Access FAQ for more information.
Siepel A, Pollard KS, and Haussler D. New methods for detecting
lineage-specific selection. In Proceedings of the 10th International
Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205.
DOI: 10.1007/11732990_17