5b156a144f9b6370354acb5e242fc64be5575af4 jnavarr5 Fri Sep 6 13:07:46 2019 -0700 Adding some headers to split the introduciton to genomics section from the more complex features of the Genome Browser, refs #20314 diff --git src/hg/htdocs/goldenPath/history.html src/hg/htdocs/goldenPath/history.html index 01af301..4ee5ac3 100755 --- src/hg/htdocs/goldenPath/history.html +++ src/hg/htdocs/goldenPath/history.html @@ -1,76 +1,84 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser History" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>UCSC Genome Browser Project History</h1> <h2>Table of Contents</h2> <ul> <li><a href="#overview">Genome Browser Overview</a></li> + <ul class="gbsNoBullet"> + <li><a href="#genomic">The Genomic Kaleidoscope</a></li> + <li><a href="#tools">Genomic Tools</a></li> + </ul> <li><a href="#race">Human Genome Project — The Race</a></li> <ul class="gbsNoBullet"> <li><a href="#celera">New challenger, Celera Genomics</a></li> <li><a href="#push">Push to the Finish Line</a></li> </ul> <li><a href="#ENCODE">The ENCODE Project</a></li> <ul class="gbsNoBullet"> <li><a href="#ucsc">UC Santa Cruz's Role</a></li> </ul> <li><a href="#primer">UCSC Genome Research Primer</a></li> <ul class="gbsNoBullet"> <li><a href="#comparative">Comparative Genomics</a></li> <li><a href="#health">Possibilities for Health</a></li> </ul> </ul> <a name="overview"></a> <h2>Genome Browser Overview</h2> <p> The UCSC Genome Browser is a web-based tool serving as a multi-powered microscope that allows researchers to view all 23 chromosomes of the human genome at any scale from a full chromosome down to an individual nucleotide. The browser integrates the work of countless scientists in laboratories worldwide, including work generated at UCSC, in an interactive, graphical display.</p> +<a name="genomic"></a> +<h3>The Genomic Kaleidoscope</h3> <p> Zoomed out, the coarse-level view of the genome shows early chromosome maps as determined by electron microscopy, then the browser drills down to levels of increasing detail, focusing first on chromosome bands. The next level detail zooms in on gene clusters, showing known and predicted genes near one another on the chromosome. Zooming in further to view a single gene shows the components of genes, the introns and exons. Finally, the browser allows researchers to view the nucleotides-the As, Cs, Gs, and Ts that make up the genome alphabet. Not only does the browser show the genome sequence, but it also delineates known areas of the genome and offers supplementary information about the genes-in effect, providing the word breaks and punctuation.</p> <p> Genome sequences are difficult to read because they consist of letter strings with no breaks or punctuation. The example below contains 7 different letters (genomes contain only 4). Can you understand what it is saying? (Line borrowed from the movie, <em><a href = "https://en.wikipedia.org/wiki/Charly" target = _blank>Charly</a></em>.)</p> <pre> THATTHATISISTHATTHATISNOTISNOTISTHATITITIS</pre> <p> With word breaks and punctuation, it starts to make sense:</p> <pre> THAT THAT IS, IS. THAT THAT IS NOT, IS NOT. IS THAT IT? IT IS!</pre> <p> The UCSC Genome Browser group played a pivotal role in bringing this extraordinary life script into the light of science. The browser presents both experimentally validated and computer-predicted genes along with dozens of lines of evidence that help scientists recognize the key features of genes and predict their function. The databases for the genome browser are updated nightly with new information generated by researchers throughout the world.</p> +<a name="tools"></a> +<h3>Genomic Tools</h3> <p> When directed to focus on a particular segment of the genome, the browser displays a range of data that are stacked vertically. At the top, it shows the chromosome number and the current position on the chromosome. Underneath, it shows several rows of data about genes that have been found experimentally or have been predicted by a number of different methods. Below those are lines of information about gene expression and regulation, followed by comparisons with the genomes of other species and other information, such as single-nucleotide polymorphisms (SNPs).</p> <p> Far from simply displaying the genetic code, the UCSC browser brings the code to life by aligning relevant areas with experimental and computational data and images. It also links to international databases, giving researchers instant access to deeper information about the genome. An experienced user can form a hypothesis and verify it in minutes using this tool. Together this information represents an extremely comprehensive view of the genome, helping scientists recognize important features of the sequence and providing strong evidence of function. For instance, the genome browser helps unravel the varied splicing patterns whereby one gene can make many different proteins. This