198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html index 3598fed35a0..c88b297f5bc 100644 --- src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html +++ src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html @@ -1,236 +1,236 @@ <h2>Description</h2> Repetitive genomic elements including Transposable Element (TE) families, Satellite, Short Tandem Repeats, and low complexity DNA as annotated by RepeatMasker. These tracks were constructed with the NCBI BLAST-derived search engine RMBlast and Dfam 3.3 database (plus T2T-CHM13-derived entries submitted to the Dfam 3.6 data release in April 2022, and HG002 chrY-derived entries not yet submitted). <p> Individual tracks are identified using the three main components of the analysis, the version of RepeatMasker, the search engine used, and finally the repeat library version. <UL> <LI>RepeatMasker version April 01 2021 open-4.1.2-p1</LI> <LI>Search Engine: RMBlast (-e ncbi) [ 2.10.0+ (March 2020) ]</LI> <LI>RepeatMasker Database: Dfam_3.3 (plus T2T-CHM13-derived entries submitted to the Dfam 3.6 data release in April 2022, and HG002 chrY-derived entries not yet submitted)</LI> </UL> <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 +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 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> <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="https://www.repeatmasker.org/" target="_blank"> https://www.repeatmasker.org/</a>. 1996-2010. </p> <p> For the discovery of the additional T2T-CHM13-derived repeats included in this track, as well as the methods (and scripts) for masking the assembly with these T2T-CHM13-derived repeats and previously known repeats: </p> <p> Hoyt SJ, et al. <a href="https://www.science.org/doi/10.1126/science.abk3112" target="_blank"> From telomere to telomere: the transcriptional and epigenetic state of human repeat elements</a>. <em>bioRxiv</em>. 2022 Apr 1. </p> <p> Hoyt SJ, et al. <a href="https://zenodo.org/record/5537106" target="_blank"> From telomere to telomere: the transcriptional and epigenetic state of human repeat elements analysis code: T2T-CHM13</a>. <em>bioRxiv</em>. 2022 Apr 1. </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>