src/hg/makeDb/trackDb/netBosTau2.html 1.3

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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>
-
-<H2>References</H2>
-<P>
-Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and 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 USA</em> <B>100</B>(20), 11484-11489 (2003).</P>
-<P>
-Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
-Haussler, D., and 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> <B>13</B>(1), 103-7 (2003).</P>
-