8c2f7318d8d821de9b2a25750586a94ab5e8c1bb lrnassar Fri Nov 15 18:50:19 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/nestedRepeats.html src/hg/makeDb/trackDb/nestedRepeats.html index f49f44e..566a5e9 100644 --- src/hg/makeDb/trackDb/nestedRepeats.html +++ src/hg/makeDb/trackDb/nestedRepeats.html @@ -1,102 +1,102 @@ <h2>Description</h2> <p> This track shows joined fragments of interrupted repeats extracted -from the output of the <a href="http://www.repeatmasker.org/" target="_blank"> +from the output of the <a href="https://www.repeatmasker.org/" target="_blank"> RepeatMasker</a> program which screens DNA sequences for interspersed repeats and low complexity DNA sequences using 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> <p> The detailed annotations from RepeatMasker are in the RepeatMasker track. This track shows fragments of original repeat insertions which have been interrupted by insertions of younger repeats or through local rearrangements. The fragments are joined using the ID column of RepeatMasker output. </p> <h2>Display Conventions and Configuration</h2> <p> In pack or full mode, each interrupted repeat is displayed as boxes (fragments) joined by horizontal lines, labeled with the repeat name. If all fragments are on the same strand, arrows are added to the horizontal line to indicate the strand. In dense or squish mode, labels and arrows are omitted and in dense mode, all items are collapsed to fit on a single row. </p> <p> Items are shaded according to the average identity score of their fragments. Usually, the shade of an item is similar to the shades of its fragments unless some fragments are much more diverged than others. The score displayed above is the average identity score, clipped to a range of 50% - 100% and then mapped to the range 0 - 1000 for shading in the browser. </p> <h2>Methods</h2> <p> UCSC has used the most current versions of the RepeatMasker software and repeat libraries available to generate these data. Note that these versions may be newer than those that are publicly available on the Internet. </p> <p> Data are generated using the RepeatMasker <em>-s</em> flag. Additional flags may be used for certain organisms. 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. +<a href="https://www.repeatmasker.org/" target="_blank"> +https://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>