62b1428915cc2c8b9acbf46a86c1248833257efe mspeir Mon Nov 17 18:50:32 2025 -0800 changing rest of genome-source references to github, refs #34485 diff --git src/hg/makeDb/trackDb/rmsk.html src/hg/makeDb/trackDb/rmsk.html index 1a33e004dd8..d6fdb5d9f66 100644 --- src/hg/makeDb/trackDb/rmsk.html +++ src/hg/makeDb/trackDb/rmsk.html @@ -6,31 +6,31 @@ 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/" +<a href="https://github.com/ucscGenomeBrowser/kent/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>