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 &quot;makeDb/doc/&quot;
+<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 &quot;?&quot; at the end of the &quot;Family&quot; or &quot;Class&quot; (for example, DNA?) signifies that
 the curator was unsure of the classification. At some point in the future,
 either the &quot;?&quot; 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>