This track shows multiple alignments of 7 human coronavirus sequences, aligned to the $Organism NCBI reference sequence SARS-CoV-2 for NC_045512.2, 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 accession identifier.
Pairwise alignments of each species to the $Organism 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.
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 $Organism sequence at those alignment positions relative to the longest non-$Organism 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:
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 # step=1Pairwise 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:
-minScore=1000 -linearGap=loose
High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net.
count | sample date |
accession | phylogenetic distance |
descriptive name |
---|---|---|---|---|
1 | 2019-12-30 | NC_045512.2 | 0.000000 | SARS-CoV-2 (2019) |
2 | 2003-04 | NC_004718.3 | 0.885159 | SARS-CoV-1 (Tor2) |
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 MultiZ/autoMZ. 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:
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