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/goldenPath/trackDescriptions/bigRmskTrackDesc.html src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html new file mode 100644 index 0000000..88f2e4d --- /dev/null +++ src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html @@ -0,0 +1,208 @@ +<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>