63130a0a315c1c10d58d741cdf534d922cece886 dschmelt Thu Sep 16 15:44:09 2021 -0700 Adding S to http to eliminate warning when searching docs refs #28175 diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index 25b65be..5f93ffe 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -26,42 +26,42 @@ <li> <h6><a href="#Sessions">Using Sessions</a></h6> <li> <h6><a href="hgGeneGraph.html">Gene and Pathway Viewer</a></h6> <li> <h6><a href="#GenomeGraphs">Genome Graphs</a></h6> </ul> <h6><a href="#TrackFormatDNA">DNA text formatting</a></h6> <h6><a href="#Convert">Converting data between assemblies</a></h6> <h6><a href="#Download">Downloading genome data</a></h6> <h6><a href="#CustomTracks">Creating and managing custom annotation tracks</a></h6> <h6><a href="#TrackHubs">Getting started on Track Hubs</a></h6> <h6><a href="#UseOneFile">Track Hubs in a single file</a></h6> <h6><a href="#VisiGeneHelp">Using the VisiGene Image Browser</a></h6> </div> <div class="col-md-8"> -<form name="googleForm1" method="get" action="http://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+' site:genome.ucsc.edu/goldenPath/help';"> +<form name="googleForm1" method="get" action="https://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+' site:genome.ucsc.edu/goldenPath/help';"> <p> Search the Genome Browser help pages: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=30 maxlength=255 value=""> <input type="submit" value="Submit"> </p> </form> -<form name="googleForm2" method="GET" action="http://www.google.com/search" onSubmit="document.googleForm2.q.value=document.googleForm2.qq.value+' site:genome.ucsc.edu/';"> +<form name="googleForm2" method="GET" action="https://www.google.com/search" onSubmit="document.googleForm2.q.value=document.googleForm2.qq.value+' site:genome.ucsc.edu/';"> <p> Search the entire Genome Browser website: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=30 maxlength=255 value=""> <input type="submit" value="Submit"> </p> </form> <p> <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">Browse</a> the Genome Browser mailing list.</p> <p> <a href="../../contacts.html">Questions and feedback are welcome</a>.</p> @@ -95,31 +95,31 @@ lead to sequence details and supplementary off-site databases. To control information overload, tracks need not be displayed in full. Tracks can be hidden, collapsed into a condensed or single-line display, or filtered according to the user's criteria. Zooming and scrolling controls help to narrow or broaden the displayed chromosomal range to focus on the exact region of interest. Clicking on an individual item within a track opens a details page containing a summary of properties and links to off-site repositories such as PubMed, GenBank, Entrez, and OMIM. The page provides item-specific information on position, cytoband, strand, data source, and encoded protein, mRNA, genomic sequence and alignment, as appropriate to the nature of the track.</p> <p> A blue navigation bar at the top of the browser provides links to several other tools and data sources. For instance, under the "View" menu, the "DNA" link enables the user to view the raw genomic DNA sequence for the coordinate range displayed in the browser window. This DNA can encode track features via elaborate text formatting options. Other links tie the Genome Browser to the BLAT alignment tool, provide access to the underlying relational database via the Table Browser, convert coordinates across different assembly dates, and open the window at the -complementary <a href="http://www.ensembl.org/" target="_blank">Ensembl</a> or +complementary <a href="http//www.ensembl.org/" target="_blank">Ensembl</a> or <a href="https://www.ncbi.nlm.nih.gov/genome/gdv/" target="_blank">NCBI Genome Data Viewer</a> annotation.</p> <p> The browser data represents an immense <a href="../credits.html">collaborative effort</a> involving thousands of people from the international biomedical research community. The UCSC Bioinformatics Group itself does no sequencing. Although it creates the majority of the annotation tracks in-house, the annotations are based on publicly available data contributed by many labs and research groups throughout the world. Several of the Genome Browser annotations are generated in collaboration with outside individuals or are contributed wholly by external research groups. UCSC's other major roles include building genome assemblies, creating the Genome Browser work environment, and serving it online. The majority of the sequence data, annotation tracks, and even software are in the public domain and are available for anyone to <a href="#Download">download</a>.</p> <p> In addition to the Genome Browser, the UCSC Genome Bioinformatics group provides several other tools for viewing and interpreting genome data: <ul>