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jnavarr5
  Fri May 31 11:41:50 2019 -0700
Updating redirected links for hg18, uiLinks cronjob.

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 <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 (&gt;= 1 kb and &gt;= 90% identity) were detected
 by identifying high-copy repeats, removing these repeats from the genomic 
 sequence (&quot;fuguization&quot;) 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 &quot;fuguization&quot; 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:&#97;r&#97;&#106;&#97;&#64;&#117;&#119;.ed&#117;">Archana Raja</A>,
 <A HREF="mailto:&#116;&#105;&#110;l&#111;&#117;&#105;&#101;&#64;&#117;.
 &#119;a&#115;&#104;&#105;&#110;&#103;&#116;&#111;&#110;.
 ed&#117;">Tin Louie</A> and
 <A HREF="mailto:&#101;&#101;e&#64;&#103;s.&#119;&#97;&#115;&#104;&#105;&#110;&#103;&#116;&#111;n.&#101;&#100;&#117;">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>