src/hg/makeDb/trackDb/genomicSuperDups.html 1.14

Index: src/hg/makeDb/trackDb/genomicSuperDups.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/genomicSuperDups.html,v
retrieving revision 1.13
retrieving revision 1.14
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--- src/hg/makeDb/trackDb/genomicSuperDups.html	10 Dec 2007 20:04:13 -0000	1.13
+++ src/hg/makeDb/trackDb/genomicSuperDups.html	5 Nov 2009 00:44:50 -0000	1.14
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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 (>= 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) in the References section below.
+<em>et al.</em> (2001) in the References section below. 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 
 <A HREF="mailto:&#120;w&#115;&#64;&#103;&#115;.w&#97;&#115;&#104;&#105;&#110;&#103;&#116;&#111;&#110;.ed&#117;">Ginger Cheng</A>, 
-<A HREF="mailto:&#120;w&#115;&#64;&#103;&#115;.w&#97;&#115;&#104;&#105;&#110;&#103;&#116;&#111;&#110;.ed&#117;">Xinwei She</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> 
+<A HREF="mailto:&#120;w&#115;&#64;&#103;&#115;.w&#97;&#115;&#104;&#105;&#110;&#103;&#116;&#111;&#110;.ed&#117;">Xinwei She</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://www.ncbi.nlm.nih.gov/pubmed/12169732?dopt=Abstract" 
+TARGET=_BLANK>Recent segmental duplications in the human genome</A>.
+<em>Science.</em> 2002 Aug 9;297(5583):1003-7.</P>
+<P>
 Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE.
 <A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11381028&dopt=Abstract" 
 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.</P>