5709a7858d5c197721be66d5218a79124abadb70 lrnassar Tue Mar 17 08:46:31 2026 -0700 Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254 diff --git src/hg/htdocs/goldenPath/help/quickLiftChain.html src/hg/htdocs/goldenPath/help/quickLiftChain.html index c3ffb71fa35..adde6990406 100644 --- src/hg/htdocs/goldenPath/help/quickLiftChain.html +++ src/hg/htdocs/goldenPath/help/quickLiftChain.html @@ -1,98 +1,98 @@ <h2>Description</h2> <p> The Alignment Differences track shows mismatches, insertions, deletions, and double-sided insertions between two assemblies. In <font color="#008000">QuickLift</font>, the <b>source assembly</b> is the assembly where the annotations come from, and the <b>destination (target) assembly</b> is the assembly you are currently viewing. <font color="#008000">QuickLift</font> maps (liftOver) annotations on demand from the source to the target using whole-genome alignment chains. </p> <h2>Display Conventions and Configuration</h2> <p> This track is part of the <font color="#008000">QuickLift</font> track group, which appears under a green "<font color="#008000">QuickLift</font> from ..." group in the target genome assembly. <font color="#008000">QuickLift</font> tracks have a green left-side button bar in the Browser graphic, instead of the usual gray, and can be removed by the <button>Disconnect</button> button. </p> <p> The Alignment Differences track displays liftOver differences using triangles and lines. Alignment differences are marked by lines, with colored triangles indicating the type of difference: </p> <ul> <li>Insertions: <font color="#407F00">green</font></li> <li>Deletions: <font color="#00007F">blue</font></li> <li>Double-sided insertions: <font color="#7F7F7F">gray</font> (Both the source and target assemblies contain unalignable sequence between two regions of aligned sequence)</li> <li>Mismatches: <font color="#FF0000">red</font></li> </ul> <div class="text-center"> - <img src="../../images/QuickLift/quickLiftTrianglesMouseOver.png" width='70%'> + <img alt="QuickLift track with triangle markers indicating alignment differences on mouseover" src="../../images/QuickLift/quickLiftTrianglesMouseOver.png" width='70%'> </div> <p> Mousing over a triangle displays the size base-pair (bp) difference and the type of alignment difference. Clicking a triangle opens a details page showing: </p> <ul> <li>Source and target assembly genome positions</li> <li>DNA sequence alignment</li> <li>Type and size of each alignment difference within the currently visible browser region</li> </ul> <div class="text-center"> -<img src="../../images/QuickLift/quickLiftAlignmentDifferences.png" width='50%'> +<img alt="QuickLift chain display highlighting base-level alignment differences between assemblies" src="../../images/QuickLift/quickLiftAlignmentDifferences.png" width='50%'> </div> <h2>Methods</h2> <p> An alignment between two DNA sequences maps every nucleotide in one sequence to a nucleotide in another sequence. By making and using whole-genome alignments (Kent et al., 2003), genome annotations can be "lifted" to another assembly (<a href="/cgi-bin/hgLiftOver" target="_blank">liftOver</a>) in bulk, one track at a time. <font color="#008000">QuickLift</font> uses the same algorithm to lift annotations on demand, in real-time, for all visible tracks. Only the annotations in the currently visible region are lifted, so this is usually fast enough when browsing a genome. </p> <p> The Alignment Differences track is generated by comparing the whole-genome alignment chain between the source and target assemblies. Where the alignment differs, the track classifies each difference by type: </p> <ul> <li><b>Insertions and Deletions</b> — gaps in the alignment where one assembly has sequence that the other does not</li> <li><b>Double-sided insertions (double gaps)</b> — both assemblies contain unalignable sequence between two aligned regions</li> <li><b>Mismatches</b> — aligned positions where the bases differ between the two assemblies</li> </ul> <p> <font color="#008000">QuickLift</font> functionality depends on the availability of alignment files (chains) that describe how sequences in one assembly correspond to another. The alignment files are currently made at UCSC, and if no alignment file is available for the assembly in which you're interested, please send a request to the <a href="/contacts.html" target="_blank" >genome mailing list</a>, and we will attempt to provide you with one. </p> <h2>References</h2> <p> Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. <a href="https://www.pnas.org/doi/10.1073/pnas.1932072100?url_ver=Z39.88- 2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed" target="_blank"> Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes</a>. <em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a> </p>