675d1eaac3a4f636444eb9e2056a1f1c5185b6c9 brianlee Fri Apr 1 16:30:36 2022 -0700 Adding a note about rmsk process from MLQ #29181 diff --git src/hg/makeDb/trackDb/rmsk.html src/hg/makeDb/trackDb/rmsk.html index 4ccc204..299c9fa 100644 --- src/hg/makeDb/trackDb/rmsk.html +++ src/hg/makeDb/trackDb/rmsk.html @@ -1,103 +1,107 @@ <h2>Description</h2> <p> This track was created by using Arian Smit's <a href="http://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.</p> +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> <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. </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>