This track shows multiple alignments of 7 human coronavirus sequences,
aligned to the SARS-CoV-2 NCBI reference sequence SARS-CoV-2 for
genome assembly GCF_009858895.2_ASM985889v3.
The multiple alignments were generated using Multiz and
other tools in the UCSC/Penn State Bioinformatics
comparative genomics alignment pipeline.
In the track display, the sequences are labeled using common names.
Note the table below to relate these common names to the NCBI assembly
Display Conventions and Configuration
Pairwise alignments of each species to the SARS-CoV-2 genome are
displayed as a series of colored blocks indicating the functional effect of polymorphisms (in pack
mode), or as a wiggle (in full mode) that indicates alignment quality.
In dense display mode, percent identity of the whole alignments is shown in grayscale using
darker values to indicate higher levels of identity.
In pack mode, regions that align with 100% identity are not shown. When there is not 100% percent
identity, blocks of four colors are drawn.
- Red blocks are
drawn when a polymorphism in a coding region results in a change in the amino
acid that is generated.
- Green blocks are
drawn when a polymorphism in a coding region results in no change to the amino
acid that is generated.
- Blue blocks are
drawn when a polymorphism is outside a coding region.
- Pale yellow blocks
are drawn when there are no aligning bases to that region in the reference
Checkboxes on the track configuration page allow selection of the
species to include in the pairwise display.
Configuration buttons are available to select all of the species
(+), deselect all of the species (-), or
use the default settings (Reset to defaults).
For text nucleotide alignments, click on
the alignment tracks. To view detailed information about the alignments at a specific
position, zoom to a small region or click the 'base' button to see amino acid alignments.
When zoomed-in to the base-level display, the track shows the amino acid
composition of each alignment.
The numbers and symbols on the Gaps
line indicate the lengths of gaps in the SARS-CoV-2 sequence at those
alignment positions relative to the longest non-SARS-CoV-2 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 can be turned off in base-level display mode if desired.
You can 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
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.
Pairwise alignments with the reference sequence were generated for
each sequence using LASTZ version 1.04.03.
Parameters used for each LASTZ alignment:
# hsp_threshold = 3000
# gapped_threshold = 3000 = L
# x_drop = 910
# y_drop = 9400 = Y
# gap_open_penalty = 400
# gap_extend_penalty = 30
# A C G T
# A 91 -114 -31 -123
# C -114 100 -125 -31
# G -31 -125 100 -114
# T -123 -31 -114 91
# seed=1110100110010101111 w/2 transitions
Pairwise alignments were then linked into chains using a dynamic programming
algorithm that finds maximally scoring chains of gapless subsections
of the alignments organized in a kd-tree. Parameters used in
the chaining (axtChain) step:
High-scoring chains were then placed along the genome, with
gaps filled by lower-scoring chains, to produce an alignment net.
|3||2012-06-13||NC_019843.3||2.434930||MERS Middle East respiratory syndrome CoV|
|4||2004-03||NC_006213.1||2.589639||Human CoV OC43 strain ATCC VR-759|
|5||2004-04||NC_006577.2||2.649716||Human CoV HKU1|
|6||2000-09||NC_002645.1||2.983896||Human CoV 229E|
|7||2004-03||NC_005831.2||3.009141||Human Coronavirus NL63|
The multiple alignment was constructed from the resulting
pairwise alignments progressively aligned using
The phylogenetic tree was calculated on 31mer frequency similarity
and neighbor joining that distance matrix with the
PHYLIP toolset command:
neighbor. The reference sequence NC_045512v2 is at the
top of the tree:
((((SARS_CoV_2 SARS_CoV_1) MERS) (OC43 HKU1)) (CoV229E NL63))
Framing tables from the genes were constructed to enable
visualization of codons in the multiple alignment display.
Downloads for data in this track are available:
This track was created using the following programs:
- Alignment tools: LASTZ (formerly Blastz) and MultiZ by Minmei Hou,
Scott Schwartz, Robert Harris, and Webb Miller of the
Penn State Bioinformatics Group
- Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and
other programs in PHAST by
Adam Siepel at Cold Spring Harbor Laboratory (original development
done at the Haussler lab at UCSC).
- Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
- MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows
by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
- Tree image generator: phyloPng by Galt Barber, UCSC
- Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle
display), and Brian Raney (gap annotation and codon framing) at UCSC
Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M,
Fullah M, Dudas G et al.
Genomic surveillance elucidates Ebola virus origin and transmission
during the 2014 outbreak.
Science 2014 Sep 12;345(6202):1369-72.
Supplemental Materials and Methods
Phylo-HMMs, phastCons, and phyloP:
Felsenstein J, Churchill GA.
A Hidden Markov Model approach to
variation among sites in rate of evolution.
Mol Biol Evol. 1996 Jan;13(1):93-104.
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A.
Detection of nonneutral substitution rates on mammalian phylogenies.
Genome Res. 2010 Jan;20(1):110-21.
PMID: 19858363; PMC: PMC2798823
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K,
Clawson H, Spieth J, Hillier LW, Richards S, et al.
Evolutionarily conserved elements in vertebrate, insect, worm,
and yeast genomes.
Genome Res. 2005 Aug;15(8):1034-50.
PMID: 16024819; PMC: PMC1182216
Siepel A, Haussler D.
Phylogenetic Hidden Markov Models.
In: Nielsen R, editor. Statistical Methods in Molecular Evolution.
New York: Springer; 2005. pp. 325-351.
A space-time process model for the evolution of DNA
Genetics. 1995 Feb;139(2):993-1005.
PMID: 7713447; PMC: PMC1206396
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
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM,
Baertsch R, Rosenbloom K, Clawson H, Green ED, et al.
Aligning multiple genomic sequences with the threaded blockset aligner.
Genome Res. 2004 Apr;14(4):708-15.
PMID: 15060014; PMC: PMC383317
LASTZ (formerly Blastz):
Chiaromonte F, Yap VB, Miller W.
Scoring pairwise genomic sequence alignments.
Pac Symp Biocomput. 2002:115-26.
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