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/rmsk.html src/hg/makeDb/trackDb/rmsk.html index 4ce3adf..1a33e00 100644 --- src/hg/makeDb/trackDb/rmsk.html +++ src/hg/makeDb/trackDb/rmsk.html @@ -1,120 +1,120 @@ <h2>Description</h2> <p> This track was created by 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 the <a href="https://www.girinst.org/repbase/update/index.html" target=_blank>Repbase Update</a> library of repeats 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. Some newer assemblies have been made with Dfam, not Repbase. You can find the details for how we make our database data here in our "makeDb/doc/" <a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/tree/master/src/hg/makeDb/doc/" target="_blank">directory</a>.</p> <p> When analyzing the data tables of this track, keep in mind that Repbase is not the same as the Repeatmasker sequence database and that the repeat names in the Repeatmasker output are not the same as the sequence names in the Repeatmasker database. Concretely, you can find a name such as "L1PA4" in the Repeatmasker output and this track, but there is not necessarily a single sequence "L1PA4" in the Repeatmasker database. This is because Repeatmasker creates annotations by joining matches to partial pieces of the database together so there is no 1:1 relationship between its sequence database and the annotations. To learn more, you can read the Repeatmasker paper, its source code or reach out to the Repeatmasker authors, your local expert on transposable elements or us. </p> <h2>Display Conventions and Configuration</h2> <p> In full display mode, this track displays up to ten different classes of repeats: <ul> <li>Short interspersed nuclear elements (SINE), which include ALUs</li> <li>Long interspersed nuclear elements (LINE)</li> <li>Long terminal repeat elements (LTR), which include retroposons</li> <li>DNA repeat elements (DNA)</li> <li>Simple repeats (micro-satellites)</li> <li>Low complexity repeats</li> <li>Satellite repeats</li> <li>RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)</li> <li>Other repeats, which includes class RC (Rolling Circle)</li> <li>Unknown</li> </ul> </p> <p> The level of color shading in the graphical display reflects 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> 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> 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" target="_blank">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> 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>