8c2f7318d8d821de9b2a25750586a94ab5e8c1bb lrnassar Fri Nov 15 18:50:19 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/joinedRmsk.html src/hg/makeDb/trackDb/joinedRmsk.html index 45d4a55..6f49523 100644 --- src/hg/makeDb/trackDb/joinedRmsk.html +++ src/hg/makeDb/trackDb/joinedRmsk.html @@ -1,471 +1,471 @@ <h2>Description</h2> <p> This track was created using Arian Smit's -<a href="http://www.repeatmasker.org/" target="_blank">RepeatMasker</a> +<a href="https://www.repeatmasker.org/" target="_blank">RepeatMasker</a> program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the <a href="http://hgdownload.soe.ucsc.edu/downloads.html" target=_blank>Downloads</a> page). RepeatMasker uses a separately curated version of the <a href="https://www.girinst.org/repbase/update/index.html" target=_blank>Repbase Update</a> repeat library from the <a href="https://www.girinst.org/" target=_blank>Genetic Information Research Institute</a> (GIRI). Repbase Update is described in Jurka (2000) in the References section below. </p> <p> Alternatively, RepeatMasker can use the new <a href="http://dfam.janelia.org/" target="_blank">Dfam</a> database of repeat profile HMMs. Profile HMMs provide a richer description of the repeat families and when used with RepeatMasker + <a href="http://hmmer.janelia.org/" target="_blank">nhmmer</a> provide a more sensitive approach to identifying repeats. Dfam is described in Wheeler <em>et al</em>. (2012) in the References section below. </p> <h2>Display Conventions and Configuration</h2> <p> In dense display mode, a single line is displayed denoting the coverage of repeats using a series of black boxes. </p> <p> In full display mode, the track view is controlled by the scale of the view. At scales between 10 Mb and 30 kb, this track displays up to ten different classes of repeats (see below) one class per line. 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. </p> <p> In full display mode and at scales less than 30 kb, a new detailed display mode is used. Repeats are displayed as arrow 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 consensus sequence. If the length of the unaligned sequence is large, a double interruption line is used to indicate that the unaligned sequence is not to scale. </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. 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x1="481.32035" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> <line id="svg_50" stroke="#fcf7f7" y2="60.74219" x2="491.38283" y1="72.11719" x1="481.88283" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> <line id="svg_51" stroke="#fffcfc" y2="60.46094" x2="501.7266" y1="49.71094" x1="491.19535" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> <line id="svg_52" stroke="#fcf7f7" y2="60.74219" x2="501.25783" y1="72.11719" x1="491.75783" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> <line id="svg_53" stroke="#fffcfc" y2="60.46094" x2="511.3516" y1="49.71094" x1="500.82035" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> <line id="svg_54" stroke="#fcf7f7" y2="60.74219" x2="510.88283" y1="72.11719" x1="501.38283" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> <line id="svg_55" stroke="#fffcfc" y2="60.48437" x2="520.26566" y1="49.73437" x1="509.7344" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> <line id="svg_56" stroke="#fcf7f7" y2="60.76562" x2="519.79689" y1="72.14062" x1="510.29689" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> </g> </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> <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> UCSC has used the most current versions of the RepeatMasker software and repeat libraries available to generate these data. Note that these versions may be newer than those that are publicly available on the Internet. </p> <p> Data are generated using the RepeatMasker <em>-s</em> flag. Additional flags may be used for certain organisms. Repeats are soft-masked. Alignments may extend through repeats, but are not permitted to initiate in them. See the <a href="/FAQ/FAQdownloads#download16">FAQ</a> for more information. </p> <h2>Credits</h2> <p> Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track. </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. +<a href="https://www.repeatmasker.org/" target="_blank"> +https://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>