+ +The UCSC Genome Browser is an open-source, interactive sequence visualization tool that +has been a cornerstone of genomics since we released the first human genome assembly +20 years ago. Cited in more than 37,000 scientific articles and used by thousands of +researchers each day; it allows for cross-referencing of research, clinical, +and epidemiology data against reference genomes, including +SARS-CoV-2. This data is continuously +updated and added to as new datasets become available. For a more thorough description, +please reference our +SARS-CoV-2 Genome Browser Nature Genetics paper. We also post updates and COVID Browser +resources to out COVID-19 Browser home page.
++This guide will go through some of the most important use cases of the SARS-CoV-2 Genome Browser. +These topics include:
++For those who prefer a video explanation, we also have the following tutorial:
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++The standardized reference genome displayed on the +COVID Genome Browser is from one of the first isolated +cases, known as NC_045512v2 or wuhCor1. With more than 80 track datasets across the +SARS-CoV-2 reference genome's nearly 30,000 RNA +bases, navigation is essential to finding the information you want to see. Below is an example +view of the SARS-CoV-2 Genome Browser with labeled sections highlighting the navigation, +reference sequence, annotations, and other available track datasets.
+ ++Navigation controls at the top allow users to move left and right and to zoom. +The search box allows users to search for particular features or to move +to exact genomic coordinates. The RNA sequence is shown at the top only when the view +is sufficiently zoomed in. Annotations are shown for data tracks that have been set to +visible in the available tracks section at the bottom. +Tracks can be configured with a right-click or by clicking on their name near the +bottom of the page.
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This is a view of the SARS-CoV-2 Genome Browser (COVID Browser) + with labeled elements to help with orientation. Interact with this session by clicking on + the picture. To read the full caption, please go to our + + Nature Genetics paper. +
+ + + ++Gene and protein annotations are organized by the contributor, most notably NCBI and UniProt. +Having multiple information sources allows a consensus to be formed among datasets. +Like many viral genomes, molecular complexity arises from polyproteins rearranging, +generating ~29 protein products. Most notable among these is the S (spike) protein which defines +coronaviruses and allows entry into cell membrane. Additional tracks contain information such +as interactions between viral proteins and human proteins (protein interact), PDB structures, and +RNA structure annotations (Rangan RNA), and more.
+ ++Sequence alignments and conservation data are also available across the SARS-CoV-2 genome, +from large-scale views to individual bases and amino acids. Four conservation +tracks compare sequences with 44 bat coronaviruses, 119 vertebrate +coronaviruses, 7 human coronaviruses, and PhyloCSF computed conservation scores. +The tracks display differently depending on visibility mode and the number of +bases on the screen.
+ ++Datasets can be turned on by setting the dropdown +next to the data track name from "hide" to dense, squish, pack, or full. Then click +the button to see these changes in effect. +Clicking on a data track name will take you to a description with more information on the +dataset, display conventions, methods, and references. Clicking on a particular item +will take you to a page with complete information about that item and dataset.
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This Genome Browser display shows some of the gene and + conservation tracks available on the SARS-CoV-2 genome. You should be able to see UniProt + protein products, regions of interest, and domains all mapped against the SARS-CoV-2 genome. + Below those tracks are two different conservation alignments in "squish" and + "pack" formats, comparing bat-host and human-host coronavirus sequences with the + reference SARS-CoV-2 genome. Interact with this session by clicking on the picture. +
+ ++The SARS-CoV-2 Genome Browser displays data on variation within SARS-CoV-2 +from UniProt, GenBank, GISAID, Nexstrain, and other providers. These datasets cover global trends +in SARS-CoV-2 variation among all available public sequences, with regional descriptions +available through clicking into a particular entry. A few of the most notable tracks under the +"Variation and Repeats" section are the +Phylogeny: Public track, which shows a +continuously updating phylogenetic tree that clusters similar sequences, with the frequency of each +mutation shown by the height of the bar at that particular base. Tools are provided to filter these +data to show only well-supported mutation calls, set thresholds for minor-allele frequency, and display +data for specific clades.
++Another track is the +spike protein mutations from community annotations, highlighted as amino acid changes with red +indicating strong antibody escape in receptor-binding domain (RBD) mutation screens. The Genome +Browser has also has the +Variants of Concern track, which +pinpoints each accumulated mutation that defines 4 strains of SARS-CoV-2 +of particular concern, labeled based on lay terms (such as 'California variant') as well as +the using the lineage defined by the +Pangolin software +(such as 'B.1.1.7').
+ ++The Genome Browser also provides 12 immunology datasets that can inform potential therapeutic +targets or public health risks. Protein epitopes are highlighted in the genome by multiple tracks, +including those from the +Immune Epitope Database (IEDB) and from +a study of COVID+ patients. +Of particular interest are the datasets describing surveys of antibody response across +a variety of SARS-CoV-2 variants in the receptor-binding domain +(Antibody Escape Mutations).
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This image shows some of the variation data tracks + that can be displayed on the SARS-CoV-2 genome, specifically zoomed into the receptor-binding domain of + the Spike protein. Validated epitopes are displayed in black that may be a target for + therapeutic antibodies. In red and black, antibody escape scores are are shown for each + genome position. Smaller tick marks show amino acid or nucleotide changes from different sources, + with more information available by clicking into the item.
+ ++The UCSC Genome Browser has developed a tool that allows placement of SARS-CoV-2 +sequences onto existing phylogenetic trees far faster than previous methods, allowing +instantaneous tracing of strains and transmission events. This tool is called +Ultrafast Sample placement on Existing tRees (UShER) and +exists as an interactive web-tool to compare sequences and link to existing public phylogenetic +trees. +
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After uploading a Fasta file, the tool returns a page with quality +metrics such as: number of bases aligned, number of Ns, and number of maximally parsimonious +placements along with the lineage and clade of the nearest neighbor. Colored boxes highlight +possible quality issues, green meaning this was a high confidence placement.
+ ++You can view your aligned SARS-CoV-2 sequence genotypes along with their closest known +relatives among the 150,000+ public sequences. You can compare among your uploaded +samples or trace possible transmission vectors using mutational signatures.
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The uploaded sequences are highlighted in blue alongside +their most closely aligned public sequences. You can investigate genotypes and relationships +between samples.
+ + + + ++Along with a suite of data tracks, filters, and visualization options for the SARS-CoV-2 +genome, the UCSC Genome Browser offers many additional ways to interface with our data. +You can upload your data on the reference genome in +nearly any format with our +Custom Track tool. If you have unaligned sequence, + you can use our BLAT +sequence alignment tool to get coordinates and base-by-base comparison +with any reference genome. We also display formatted data +as Track Hubs and curate a list of +user-submitted Public Track Hubs. +
++As part of our open-source, open-access philosophy, we try to make it as easy as possible +for researchers to download entire datasets or filtered subsets. Each track description page +has a Data Access section which points users to our main options for data download. +For downloading complete datasets, our +SARS-CoV-2 download +directory provides access to all our source files for transparency and reproducibility. +Our Table Browser tool lets users interact with our +data using a variety of filters based on score, identifiers, or any other field. Table Browser +also allows users to convert data into multiple different formats (e.g. BED, GTF) and to access +different formatted sequence outputs (in FASTA format).
+ ++We have a JSON API which can be programmatically called and return +any dataset in its entirety or as a filtered subset based on documented input parameter. We also +offer a Public SQL server for similar flexible, automatic way to access +genomic data and annotations. Along with this particular virus genome browser, we have thousands of +genomes available for visualization and analysis from our +genome assemblies gateway page. +
+ + ++The Genome Browser offers rapid email support for anything related to our tools. If your +question is general or may have been asked before, please review our +Browser documentation and our archive +of +previously answered questions. If you would still like help, please go to +our Contact Us page to see access our email support. When contacting us, +please include a session link, images, and example data if applicable. We are active on +social media, you can follow us on Twitter +or Facebook.
+ ++We are always looking to collaborate with researchers and add new datasets to our site. +We also seek to continuously improve our tools to meet the needs of the scientific community. +If you have any collaboration ideas, contributions, or feature requests, please reach out through +our suggestion page.
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