d2a02f56a0e84d51213d44955b694ce7daace230 jnavarr5 Fri May 31 11:41:50 2019 -0700 Updating redirected links for hg18, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/genomicSuperDups.html src/hg/makeDb/trackDb/genomicSuperDups.html index 32da41e..41a72ab 100644 --- src/hg/makeDb/trackDb/genomicSuperDups.html +++ src/hg/makeDb/trackDb/genomicSuperDups.html @@ -1,67 +1,67 @@ <H2>Description</H2> <P> This track shows regions detected as putative genomic duplications within the golden path. The following display conventions are used to distinguish levels of similarity: <UL> <LI> Light to dark gray: 90 - 98% similarity <LI> Light to dark yellow: 98 - 99% similarity <LI> Light to dark orange: greater than 99% similarity <LI> Red: duplications of greater than 98% similarity that lack sufficient Segmental Duplication Database evidence (most likely missed overlaps) </UL> For a region to be included in the track, at least 1 Kb of the total sequence (containing at least 500 bp of non-RepeatMasked sequence) had to align and a sequence identity of at least 90% was required.</P> <H2>Methods</H2> <P> Segmental duplications play an important role in both genomic disease and gene evolution. This track displays an analysis of the global organization of these long-range segments of identity in genomic sequence. </P> <P>Large recent duplications (>= 1 kb and >= 90% identity) were detected by identifying high-copy repeats, removing these repeats from the genomic sequence ("fuguization") and searching all sequence for similarity. The repeats were then reinserted into the pairwise alignments, the ends of alignments trimmed, and global alignments were generated. For a full description of the "fuguization" detection method, see Bailey <em>et al.</em>, 2001. This method has become known as WGAC (whole-genome assembly comparison); for example, see Bailey <em>et al.</em>, 2002. <H2>Credits</H2> <P> These data were provided by Ginger Cheng, Xinwei She, <A HREF="mailto:araja@uw.edu">Archana Raja</A>, <A HREF="mailto:tinlouie@u. washington. edu">Tin Louie</A> and <A HREF="mailto:eee@gs.washington.edu">Evan Eichler</A> at the <A HREF="http://eichlerlab.gs.washington.edu/" TARGET=_BLANK>University of Washington</A>. </P> <H2>References</H2> <P> Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. -<A HREF="http://science.sciencemag.org/content/297/5583/1003" +<A HREF="https://science.sciencemag.org/content/297/5583/1003" TARGET=_BLANK>Recent segmental duplications in the human genome</A>. <em>Science</em>. 2002 Aug 9;297(5583):1003-7. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12169732" target="_blank">12169732</a> </p> <P> Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. <A HREF="https://genome.cshlp.org/content/11/6/1005.long" TARGET=_blank>Segmental duplications: organization and impact within the current human genome project assembly</A>. <em>Genome Res</em>. 2001 Jun;11(6):1005-17. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11381028" target="_blank">11381028</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC311093/" target="_blank">PMC311093</a> </p>