src/hg/makeDb/trackDb/netHg19.html 1.1

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+<H2>Description</H2>
+<P>
+This track shows the best $o_organism/$organism chain for 
+every part of the $organism genome. It is useful for
+finding orthologous regions and for studying genome
+rearrangement.  The $o_organism sequence used in this annotation is from
+the $o_date ($o_db) assembly.</P>
+
+<H2>Display Conventions and Configuration</H2>
+<P>
+In full display mode, the top-level (level 1)
+chains are the largest, highest-scoring chains that
+span this region.  In many cases gaps exist in the
+top-level chain.  When possible, these are filled in by
+other chains that are displayed at level 2.  The gaps in 
+level 2 chains may be filled by level 3 chains and so
+forth. </P>
+<P>
+In the graphical display, the boxes represent ungapped 
+alignments; the lines represent gaps.  Click
+on a box to view detailed information about the chain
+as a whole; click on a line to display information
+about the gap.  The detailed information is useful in determining
+the cause of the gap or, for lower level chains, the genomic
+rearrangement. </P> 
+<P> 
+Individual items in the display are categorized as one of four types
+(other than gap):</P>
+<P><UL>
+<LI><B>Top</B> - the best, longest match. Displayed on level 1.
+<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above
+it.
+<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in 
+the opposite orientation.
+<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the 
+level above.
+</UL></P>
+
+<H2>Methods</H2>
+<P>
+Chains were derived from blastz alignments, using the methods
+described on the chain tracks description pages, and sorted with the 
+highest-scoring chains in the genome ranked first. The program
+chainNet was then used to place the chains one at a time, trimming them as 
+necessary to fit into sections not already covered by a higher-scoring chain. 
+During this process, a natural hierarchy emerged in which a chain that filled 
+a gap in a higher-scoring chain was placed underneath that chain. The program 
+netSyntenic was used to fill in information about the relationship between 
+higher- and lower-level chains, such as whether a lower-level
+chain was syntenic or inverted relative to the higher-level chain. 
+The program netClass was then used to fill in how much of the gaps and chains 
+contained <em>N</em>s (sequencing gaps) in one or both species and how much
+was filled with transposons inserted before and after the two organisms 
+diverged.</P>
+
+<H2>Credits</H2>
+<P>
+The chainNet, netSyntenic, and netClass programs were
+developed at the University of California
+Santa Cruz by Jim Kent.</P>
+<P>
+Blastz was developed at <A HREF="http://bio.cse.psu.edu"
+TARGET=_blank>Pennsylvania State University</A> by
+Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from
+Ross Hardison.</P>
+<P>
+Lineage-specific repeats were identified by Arian Smit and his program 
+<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>.</P>
+<P>
+The browser display and database storage of the nets were made
+by Robert Baertsch and Jim Kent.</P>
+
+<H2>References</H2>
+<P>
+Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
+<A HREF="http://www.pnas.org/cgi/content/abstract/1932072100v1"
+TARGET=_blank>Evolution's cauldron: Duplication, deletion, and rearrangement
+in the mouse and human genomes</A>.
+<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.</P>
+<P>
+Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,
+Haussler D, Miller W.
+<A HREF="http://www.genome.org/cgi/content/abstract/13/1/103"
+TARGET=_blank>Human-Mouse Alignments with BLASTZ</A>.
+<em>Genome Res.</em> 2003 Jan;13(1):103-7.</P>
+