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 "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>