2dc16c959a1a517aaae8649c2ca0de10a2ddd96b dschmelt Thu Mar 11 00:50:45 2021 -0800 Next addition to covid browser intro refs #27174 diff --git src/hg/htdocs/goldenPath/help/covidBrowserIntro.html src/hg/htdocs/goldenPath/help/covidBrowserIntro.html index e3c4c98..5a9128e 100755 --- src/hg/htdocs/goldenPath/help/covidBrowserIntro.html +++ src/hg/htdocs/goldenPath/help/covidBrowserIntro.html @@ -85,31 +85,31 @@ tracks which compare sequence similarity of 44 bat coronaviruses, 119 vertebrate coronaviruses, PhyloCSF computed conservation scores, and alignments of 7 human coronaviruses. The tracks have different displays depending on visibility mode and number of bases on the screen.</p> <p> 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>refresh</button> 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.</p> </div> <div class="col-md-6"> -<p class="text-left"> +<p class="text-center"> <a href="http://genome.ucsc.edu/s/dschmelt/covidBrowserIntroGenes"><img class="text-center" src="../../images/covidBrowserIntroGenes.png" alt="Some of the gene and conservation data on the Genome Browser" width="800" height="427"></a> <p class="gbsCaption text-center">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. </p> </p> </div> </div> <a name="var"></a> @@ -134,23 +134,62 @@ of particular concern, labeled based on lay terms (such as 'California variant') as well as the using the lineage defined by the <a href="https://github.com/cov-lineages/pangolin/" target="_blank">Pangolin software</a> (such as 'B.1.1.7').</p> <p> 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 <a href="https://www.iedb.org/" target="_blank"> Immune Epitope Database (IEDB)</a> and from <a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=targets">a study of COVID+ patients</a>. Of particular interest are the datasets describing surveys of antibody response across a variety of SARS-CoV-2 variants in the receptor binding domain (<a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=abEscape">Antibody Escape Mutations</a>).</p> +<p class="text-center"> + <a href="http://genome.ucsc.edu/s/dschmelt/covidBrowserIntroVars"><img class="text-center" + src="../../images/covidBrowserIntroVars.png" + alt="Some of the variation and immunology data on the Genome Browser" width="800" height="427"></a> + <p class="gbsCaption text-center">This image is an example of some of the variation data tracks + that can be displayed on the SARS-CoV-2 genome, zoomed into the receptor binding domain (RBD) 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.</p> + <a name="usher"></a> -<h2>Genetic Contact Tracing with hgPhyloPlace</h2> +<h2>Genetic Contact Tracing with UShER</h2> +<p> +The UCSC Genome Browser also 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 +<a href="../../cgi-bin/hgPhyloPlace">Ultrafast Sample placement on Existing tRees (UShER)</a> and +exists as an interactive web-tool to compare sequences and link to existing public phylogenetic +trees. +<p class="text-center"> + <a href="./../cgi-bin/hgPhyloPlace"><img class="text-center" + src="../../images/covidBrowserIntroUShER.png" + alt="Example of the UShER phylogeny placement tool" width="800" + height="427"></a> + <p class="gbsCaption text-center">After uploading a Fasta file, the tool returns a page with quality +metrics like number of bases aligned, number of Ns, and number of maximally parsimonious +placements along with the lineage and clade of the neares neighbor. Colored boxes highlight +possible quality issues, green meaning this was a high confidence placement.</p> +<p> +Next, you can view your aligned SARS-CoV-2 sequence genotypes along with their closest known +relatives among the 150,000+ public sequences. You can look at compare among your uploaded samples or trace possible +transmission vectors using mutational signitures.</p> +<p class="text-center"> + <a href="./../s/dschmelt/covidBrowserIntroUShER2"><img class="text-center" + src="../../images/covidBrowserIntroUShER2.png" + alt="Example of the UShER phylogeny placement tool tree features" width="800" + height="427"></a> + <p class="gbsCaption text-center">The uploaded sequences are highlighted in blue alongside +their most closely aligned public sequences. You can investigate genotypes and relationships +between samples.</p> <h2>API, SQL, Downloads, Custom Tracks</h2> <h2>Support Docs, Contact Us</h2> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->