8b8e3dd40b5f555d315dafce8a4bd64ad07bb1b2 dschmelt Fri Sep 9 12:51:21 2022 -0700 Proofread and edited for clarity refs #29356 diff --git src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html index 88f2e4d..d6c1ca1 100644 --- src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html +++ src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html @@ -1,208 +1,211 @@ <h2>Description</h2> <p> Repetitive genomic elements including Transposable Element (TE) families, Satellite, Short Tandem Repeats, -and low complexity DNA as annotated by RepeatMasker. - - + and low complexity DNA as annotated by RepeatMasker.</p> <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. + 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 + 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 separate 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 + 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 + 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. + is large, an interruption 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> + + <td bgcolor="#1F77B4"></td> + <td align="left"><b>SINE</b> - Short Interspersed Nuclear Element</td> </tr> <tr> - <th bgcolor="#FF7F0E"></th> - <th align="left">LINE - Long Interspersed Nuclear Element</th> + <td bgcolor="#FF7F0E"></td> + <td align="left"><b>LINE</b> - Long Interspersed Nuclear Element</td> </tr> <tr> - <th bgcolor="#2CA02C"></th> - <th align="left">LTR - Long Terminal Repeat</th> + <td bgcolor="#2CA02C"></td> + <td align="left"><b>LTR</b> - Long Terminal Repeat</td> </tr> <tr> - <th bgcolor="#D62728"></th> - <th align="left">DNA - DNA Transposon</th> + <td bgcolor="#D62728"></td> + <td align="left"><b>DNA</b> - DNA Transposon</td> </tr> <tr> - <th bgcolor="#9467BD"></th> - <th align="left">Simple - Single Nucleotide Stretches and Tandem Repeats</th> + <td bgcolor="#9467BD"></td> + <td align="left"><b>Simple</b> - Single Nucleotide Stretches and Tandem Repeats</td> </tr> <tr> - <tr> - <th bgcolor="#8C564B"></th> - <th align="left">Low_complexity - Low Complexity DNA</th> + <td bgcolor="#8C564B"></td> + <td align="left"><b>Low_complexity</b> - Low Complexity DNA</td> </tr> <tr> - <th bgcolor="#E377C2"></th> - <th align="left">Satellite - Satellite Repeats</th> + <td bgcolor="#E377C2"></td> + <td align="left"><b>Satellite</b> - Satellite Repeats</td> </tr> <tr> - <th bgcolor="#7F7F7F"></th> - <th align="left">RNA - RNA Repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)</th> + <td bgcolor="#7F7F7F"></td> + <td align="left"><b>RNA</b> - RNA Repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)</td> </tr> <tr> - <th bgcolor="#BCBD22"></th> - <th align="left">Other - Other Repeats (including class RC - Rolling Circle)</th> + <td bgcolor="#BCBD22"></td> + <td align="left"><b>Other</b> - Other Repeats (including class RC - Rolling Circle)</td> </tr> <tr> - <th bgcolor="#17BECF"></th> - <th align="left">Unknown - Unknown Classification</th> + <td bgcolor="#17BECF"></td> + <td align="left"><b>Unknown</b> - Unknown Classification</td> </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. + 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>