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
@@ -3,31 +3,35 @@
 <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>