a6b50639f42d157408a1dc49512b77546b58afac lrnassar Thu Aug 25 14:18:37 2022 -0700 Moving the track description page to a new directory for tidyness, refs #29356 diff --git src/hg/htdocs/bigRmskTrackDesc.html src/hg/htdocs/bigRmskTrackDesc.html deleted file mode 100644 index 88f2e4d..0000000 --- src/hg/htdocs/bigRmskTrackDesc.html +++ /dev/null @@ -1,208 +0,0 @@ -<h2>Description</h2> -<p> -Repetitive genomic elements including Transposable Element (TE) families, Satellite, Short Tandem Repeats, -and low complexity DNA as annotated by RepeatMasker. - - - -<h2>Display Conventions and Configuration</h2> - - -<h4>Context Sensitive Zooming</h4> -<p> -This track employs a technique which chooses the appropriate visual representation for the data based on the -zoom scale, and or the number of annotations currently in view. The track will automatically switch from the -most detailed visualization ('Full' mode) to the denser view ('Pack' mode) when the window size is greater -than 45kb of sequence. It will further switch to the even denser single line view ('Dense' mode) if more than -500 annotations are present in the current view. -</p> -<h4>Dense Mode Visualization</h4> -<p> -In dense display mode, a single line is displayed denoting the coverage of repeats using a series -of colored boxes. The boxes are colored based on the classification of the repeat (see below for legend). -<br> -<br> -<img height="30" width="1250" src="/images/rmskDense.png"> -</p> -<h4>Pack Mode Visualization</h4> -<p> -In pack mode, repeats are represented as sets of joined features. These are color coded as above based on the -class of the repeat, and the further details such as orientation (denoted by chevrons) and a family label are provided. -This family label may be optionally turned off in the track configuration. -<br> -<br> -<img height="100" width="1250" src="/images/rmskPack.png"> -<br> -<br> -The pack display mode may also be configured to resemble the original UCSC repeat track. In this visualization -repeat features are grouped by classes (see below), and displayed on seperate track lines. The repeat ranges are -denoted as grayscale boxes, reflecting both the size of the repeat and -the amount of base mismatch, base deletion, and base insertion associated with a repeat element. -The higher the combined number of these, the lighter the shading. -<br> -<br> -<img height="100" width="1250" src="/images/rmskOrigPack.png"> -</p> -<h4>Full Mode Visualization</h4> -<p> -In the most detailed visualization repeats are displayed as chevron boxes, indicating the size and orientation of -the repeat. The interior grayscale shading represents the divergence of the repeat (see above) while the outline color -represents the class of the repeat. Dotted lines above the repeat and extending left or right -indicate the length of unaligned repeat model sequence and provide context for where a repeat fragment originates in its -consensus or pHMM model. If the length of the unaligned sequence -is large, an iterruption line and bp size is indicated instead of drawing the extension to scale. -<br> -<br> -<img height="125" width="1250" src="/images/rmskFull.png"> -</p> -<p> -For example, the following repeat is a SINE element in the forward orientation with average -divergence. Only the 5' proximal fragment of the consensus sequence is aligned to the genome. -The 3' unaligned length (384bp) is not drawn to scale and is instead displayed using a set of -interruption lines along with the length of the unaligned sequence. -</p> - -<img src="/images/rmskExample1.svg"> - -<p> -Repeats that have been fragmented by insertions or large internal deletions are now represented -by join lines. In the example below, a LINE element is found as two fragments. The solid -connection lines indicate that there are no unaligned consensus bases between the two fragments. -Also note these fragments form the 3' extremity of the repeat, as there is no unaligned consensus -sequence following the last fragment. -</p> - -<img src="/images/rmskExample2.svg"> - -<p> -In cases where there is unaligned consensus sequence between the fragments, the repeat will look like -the following. The dotted line indicates the length of the unaligned sequence between the two -fragments. In this case the unaligned consensus is longer than the actual genomic distance between -these two fragments. -</p> - -<img src="/images/rmskExample3.svg"> - -<p> -If there is consensus overlap between the two fragments, the joining lines will be drawn to indicate -how much of the left fragment is repeated in the right fragment. -</p> - -<img src="/images/rmskExample4.svg"> - -<p> -The following table lists the repeat class colors: -</p> - -<table> - <thead> - <tr> - <th style="border-bottom: 2px solid #6678B1;">Color</th> - <th style="border-bottom: 2px solid #6678B1;">Repeat Class</th> - </tr> - </thead> - <tr> - <th bgcolor="#1F77B4"></th> - <th align="left">SINE - Short Interspersed Nuclear Element</th> - </tr> - <tr> - <th bgcolor="#FF7F0E"></th> - <th align="left">LINE - Long Interspersed Nuclear Element</th> - </tr> - <tr> - <th bgcolor="#2CA02C"></th> - <th align="left">LTR - Long Terminal Repeat</th> - </tr> - <tr> - <th bgcolor="#D62728"></th> - <th align="left">DNA - DNA Transposon</th> - </tr> - <tr> - <th bgcolor="#9467BD"></th> - <th align="left">Simple - Single Nucleotide Stretches and Tandem Repeats</th> - </tr> - <tr> - - <tr> - <th bgcolor="#8C564B"></th> - <th align="left">Low_complexity - Low Complexity DNA</th> - </tr> - <tr> - <th bgcolor="#E377C2"></th> - <th align="left">Satellite - Satellite Repeats</th> - </tr> - <tr> - <th bgcolor="#7F7F7F"></th> - <th align="left">RNA - RNA Repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)</th> - </tr> - <tr> - <th bgcolor="#BCBD22"></th> - <th align="left">Other - Other Repeats (including class RC - Rolling Circle)</th> - </tr> - <tr> - <th bgcolor="#17BECF"></th> - <th align="left">Unknown - Unknown Classification</th> - </tr> -</table> - - -<p> -A "?" at the end of the "Family" or "Class" (for example, DNA?) -signifies that the curator was unsure of the classification. At some point in the future, -either the "?" will be removed or the classification will be changed.</p> - -<h2>Methods</h2> - -<p> -The RepeatMasker (<a href="www.repeatmasker.org">www.repeatmasker.org</a>) tool was used to generate the datasets found on this track hub. -</p> - -<h2>References</h2> - -<p> -Smit AFA, Hubley R, Green P. <em>RepeatMasker Open-3.0</em>. -<a href="http://www.repeatmasker.org" target="_blank"> -http://www.repeatmasker.org</a>. 1996-2010. -</p> - -<p> -Dfam is described in: -</p> -<p> -Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD. -<a href="https://academic.oup.com/nar/article/41/D1/D70/1073076/Dfam-a-database-of-repetitive-DNA-based-on-profile" target="_blank"> -Dfam: a database of repetitive DNA based on profile hidden Markov models</a>. -<em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D70-82. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23203985" target="_blank">23203985</a>; PMC: <a -href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531169/" target="_blank">PMC3531169</a> -</p> - -<p> -Repbase Update is described in: -</p> -<p> -Jurka J. -<a href="https://www.sciencedirect.com/science/article/pii/S016895250002093X" target="_blank"> -Repbase Update: a database and an electronic journal of repetitive elements</a>. -<em>Trends Genet</em>. 2000 Sep;16(9):418-420. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10973072" target="_blank">10973072</a> -</p> - -<p> -For a discussion of repeats in mammalian genomes, see: -</p> -<p> -Smit AF. -<a href="https://www.sciencedirect.com/science/article/pii/S0959437X99000313" target="_blank"> -Interspersed repeats and other mementos of transposable elements in mammalian genomes</a>. -<em>Curr Opin Genet Dev</em>. 1999 Dec;9(6):657-63. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10607616" target="_blank">10607616</a> -</p> - -<p> -Smit AF. -<a href="https://www.sciencedirect.com/science/article/pii/S0959437X9680030X" target="_blank"> -The origin of interspersed repeats in the human genome</a>. -<em>Curr Opin Genet Dev</em>. 1996 Dec;6(6):743-8. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/8994846" target="_blank">8994846</a> -</p>