e1428851a49899cefeeb3ed621aa19ea93334cdd gperez2 Wed Feb 18 22:09:18 2026 -0800 Updating the Alignment Differences track description page, refs #36942 diff --git src/hg/htdocs/goldenPath/help/quickLiftChain.html src/hg/htdocs/goldenPath/help/quickLiftChain.html index 45c401b59df..44e21101257 100644 --- src/hg/htdocs/goldenPath/help/quickLiftChain.html +++ src/hg/htdocs/goldenPath/help/quickLiftChain.html @@ -1,3 +1,72 @@ <h2>Description</h2> <p> -This track shows mismatches between the assembly from which the track was quickLifted and the current genome. +The Alignment Differences track shows mismatches and indels between the assembly from which the +track was QuickLifted and the current genome. +</p> + +<h2>Display Conventions and Configuration</h2> +<p> +Visible tracks, custom tracks, and track hubs on the Browser graphic page are carried over (lifted) +to the new assembly using the <font color="#008000">QuickLift</font> tracks checkbox. When a single +track from a container track, such as a superTrack or composite, is lifted, the entire container +track is carried over to the new assembly. +</p> +<font color="#008000">QuickLift</font> tracks appear under a green +"<font color="#008000">QuickLift</font> from ..." group in the New assembly. +<font color="#008000">QuickLift</font> tracks can be removed by the +<button>Disconnect</button> button. <font color="#008000">QuickLift</font> tracks have a green +left-side button bar in the Browser graphic, instead of the usual gray. +</p> +<p> +The "Alignment Differences" track displays liftOver differences using triangles and +lines; mousing over a triangle displays base-pair (bp) information. Lines and triangles are +color-coded as follows: +</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></li> + + <li>Mismatches: + <font color="#FF0000">red</font></li> +</ul> + <div class="text-center"> + <img src="../../images/QuickLift/quickLiftTrianglesMouseOver.png" width='70%'> + </div> +<p>Clicking a triangle provides additional information about the alignment.</p> + +<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> is a tool that uses the same algorithm, but it maps +("liftOver") 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> +<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, but we are working on making the pipeline to align two genomes more widely +available. +</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>