src/hg/makeDb/trackDb/rmsk.html 1.21

Index: src/hg/makeDb/trackDb/rmsk.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/rmsk.html,v
retrieving revision 1.20
retrieving revision 1.21
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--- src/hg/makeDb/trackDb/rmsk.html	2 Aug 2007 20:57:24 -0000	1.20
+++ src/hg/makeDb/trackDb/rmsk.html	4 Jun 2009 22:02:04 -0000	1.21
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 <H2>Description</H2>
 <P>
 This track was created by using Arian Smit's <A
 HREF="http://www.repeatmasker.org/"
 TARGET=_blank>RepeatMasker</A> 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, as well as a modified version of the query sequence 
-in which all the annotated repeats have been masked. RepeatMasker uses 
-the <A HREF="http://www.girinst.org/Repbase_Update.html"
+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.cse.ucsc.edu/downloads.html"
+TARGET=_BLANK>Downloads</A> page). RepeatMasker uses the
+<A HREF="http://www.girinst.org/Repbase_Update.html"
 TARGET=_blank>RepBase</A> library of repeats from the 
 <A HREF="http://www.girinst.org/" TARGET=_blank>Genetic 
 Information Research Institute</A> (GIRI).  
 RepBase is described in Jurka, J. (2000) in the References section below.</P>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 In full display mode, this track displays up to ten different classes of repeats:
 <UL>
 <LI>Short interspersed nuclear elements (SINE), which include ALUs
 <LI>Long interspersed nuclear elements (LINE)
 <LI>Long terminal repeat elements (LTR), which include retroposons
 <LI>DNA repeat elements (DNA)
 <LI>Simple repeats (micro-satellites)
 <LI>Low complexity repeats
 <LI>Satellite repeats
 <LI>RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
 <LI>Other repeats, which includes class RC (Rolling Circle)
 <LI>Unknown
 </UL></P>
 <P>
 The level of color shading in the graphical display reflects the amount of 
 base mismatch, base deletion, and base insertion associated with a repeat 
 element. The higher the combined number of these, the lighter the shading.</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.  Repeats are soft-masked. Alignments may 
 extend through repeats, but are not permitted to initiate in them. 
 See the 
 <A HREF="../FAQ/FAQdownloads#download16">FAQ</A> for 
 more information. </P>
 
 <H2>Credits</H2>
 <P>
 Thanks to Arian Smit and GIRI
 for providing the tools and repeat libraries used to generate this track.</P>
 
 <H2>References</H2>
 <P>
 Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0.
 <A HREF="http://www.repeatmasker.org" 
 TARGET=_BLANK>http://www.repeatmasker.org</A>. 1996-2007.
 </P>
 <P>
 RepBase is described in 
 Jurka J. 
 <A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10973072"
 TARGET=_blank>Repbase update: a database and an electronic journal of 
 repetitive elements</A>. 
 <em>Trends Genet</em>. 2000 Sep;16(9):418-420.</P>
 <P>
 For a discussion of repeats in mammalian genomes, see: 
 <P>
 Smit AF. <A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10607616"
 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.</P>
 <P>
 Smit AF. <A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8994846"
 TARGET=_blank>The origin of interspersed repeats in the human genome</A>. 
 <em>Curr Opin Genet Dev</em>. 1996 Dec;6(6):743-8.
 </P>