src/hg/makeDb/trackDb/netPanTro2.html 1.2

Index: src/hg/makeDb/trackDb/netPanTro2.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/netPanTro2.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/makeDb/trackDb/netPanTro2.html	7 Jul 2006 19:45:57 -0000	1.1
+++ src/hg/makeDb/trackDb/netPanTro2.html	12 Jun 2009 20:21:14 -0000	1.2
@@ -1,87 +1,87 @@
 <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, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.
+Kent WJ, 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>
+<EM>Proc Natl Acad Sci USA</EM>, 2003, 100(20):11484-9.</P>
 <P>
-Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
-Haussler, D., and Miller, W.
+Schwartz S, Kent WJ, 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>
+<EM>Genome Res.</EM>, 2003, 13(1):103-7.</P>