This information is over 2 years old. Information was current at time of publication.{"id":12896,"date":"2020-06-16T13:56:46","date_gmt":"2020-06-16T17:56:46","guid":{"rendered":"https:\/\/info.hsls.pitt.edu\/updatereport\/?p=12896"},"modified":"2020-06-25T10:55:19","modified_gmt":"2020-06-25T14:55:19","slug":"ucsc-genome-browser-tutorials-back-to-basics-exploring-sars-cov-2","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/updatereport\/ucsc-genome-browser-tutorials-back-to-basics-exploring-sars-cov-2\/","title":{"rendered":"UCSC Genome Browser Tutorials: Back to Basics and Exploring SARS-CoV-2"},"content":{"rendered":"<p><a href=\"https:\/\/genome.ucsc.edu\/index.html\"><img loading=\"lazy\" decoding=\"async\" class=\"alignright\" src=\"https:\/\/ucscgenomics.soe.ucsc.edu\/wp-content\/uploads\/genome-browse-logo.png\" alt=\"Go to UCSC Genome Browser\" width=\"253\" height=\"42\" data-emailimage=\"right\" \/><\/a>For 20 years, the University of California-Santa Cruz Genome Browser (<a href=\"https:\/\/genome.ucsc.edu\/index.html\">UCSC Genome Browser<\/a>) has provided free public access to the human genome assembly and the information it contains via a comprehensive and well-utilized graphical viewing tool. Developed and maintained by the <a href=\"https:\/\/genome.ucsc.edu\/staff.html\">Genome Bioinformatics Group<\/a> within the UCSC Genomics Institute, it has grown over the years to include a large collection of tools for viewing, analyzing, and downloading data from a broad array of vertebrate and model organism assemblies and annotations.<\/p>\n<p>The UCSC Genome Browser group recently created a three-part video series designed to explain the Browser to new users. Previous videos primarily focused on answering specific task-related questions for experienced users and introducing new features. This new series fills in the background with more basic information.<!--more--><\/p>\n<ul>\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=NBDMNv2KFik&amp;feature=youtu.be&amp;list=UUQnUJepyNOw0p8s2otX4RYQ\">Part One: Getting around in the Browser<\/a> (15:55)\n<ul>\n<li>Focuses on using accession numbers and genomic annotation identifiers in various formats to navigate the Browser.<\/li>\n<li>Examples include gene names, genomic coordinates, codon numbers, SNP rsIDs, and RefSeq NM identifiers.<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=cYys5iXN0NY&amp;feature=youtu.be&amp;list=UUQnUJepyNOw0p8s2otX4RYQ\">Part Two: Configuring the Browser<\/a> (11:57)\n<ul>\n<li>Presents configuration options geared toward making the Browser look the way you want and for making the graphic image suitable for export.<\/li>\n<li>Examples include changing font size and screen width, removing blue guidelines, and navigating quickly to nearby annotations.<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=I25Q136d6NU&amp;feature=youtu.be&amp;list=UUQnUJepyNOw0p8s2otX4RYQ\">Part Three: Configuration + DNA Navigation<\/a> (14:08)\n<ul>\n<li>Explores ways to configure the graphical viewer and looks at ways to use DNA sequences to find a location on a reference genomic assembly.<\/li>\n<li>Examples include BLAT, Short Match, Drag-N-Highlight, removing highlights, Drag-N-Zoom, configuring the scale bar\/base position track, and adding a title to an image.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p>All three tutorials are available on the <a href=\"https:\/\/www.youtube.com\/channel\/UCQnUJepyNOw0p8s2otX4RYQ\/videos\">UCSC Genome Browser YouTube channel<\/a> and include a transcript and time-stamped content outline.<\/p>\n<p>The UCSC Genome Browser group also recently added a <a href=\"https:\/\/www.youtube.com\/watch?v=Ee6h0xyZDOM&amp;feature=youtu.be&amp;list=UUQnUJepyNOw0p8s2otX4RYQ\">video and transcript<\/a> using the context of SARS-CoV-2 genome assembly to describe Browser features for the benefit of virologists and molecular biologists developing Coronavirus assays and vaccines. The tour highlights RT-PCR data, UniProt, crowd-sourced data, T-cell Reactive epitopes, and comparative genomics data for global viral isolates and those infecting non-human vertebrates. More information on the <a href=\"https:\/\/genome.ucsc.edu\/covid19.html\">UCSC SARS-CoV-2 Genome Browser<\/a> is available in a <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.05.04.075945v1\">manuscript<\/a> posted on the preprint server, bioRxiv.<\/p>\n<p>~Carrie Iwema<\/p>\n","protected":false},"excerpt":{"rendered":"<p>For 20 years, the University of California-Santa Cruz Genome Browser (UCSC Genome Browser) has provided free public access to the human genome assembly and the information it contains via a comprehensive and well-utilized graphical viewing tool. Developed and maintained by the Genome Bioinformatics Group within the UCSC Genomics Institute, it has grown over the years [&hellip;]<\/p>\n","protected":false},"author":4,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"issue-archives","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[153],"tags":[-1],"class_list":["post-12896","post","type-post","status-publish","format-standard","hentry","category-july-2020","avhec_catgroup-issue-archives"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/12896","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/comments?post=12896"}],"version-history":[{"count":6,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/12896\/revisions"}],"predecessor-version":[{"id":12926,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/12896\/revisions\/12926"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/media?parent=12896"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/categories?post=12896"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/tags?post=12896"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}