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

Index: src/hg/makeDb/trackDb/humanChainNet.html
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/humanChainNet.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/makeDb/trackDb/humanChainNet.html	2 Jun 2009 21:15:47 -0000	1.1
+++ src/hg/makeDb/trackDb/humanChainNet.html	4 Jun 2009 19:12:16 -0000	1.2
@@ -77,9 +77,9 @@
 <H3>Chain track</H3>
 <P>
 Transposons that have been inserted since the human/$organism
 split were removed from the assemblies. The abbreviated genomes were
-aligned with blastz, and the transposons were added back in.
+aligned with lastz, and the transposons were added back in.
 The resulting alignments were converted into axt format using the lavToAxt
 program. The axt alignments were fed into axtChain, which organizes all
 alignments between a single human chromosome and a single
 $organism chromosome into a group and creates a kd-tree out
@@ -88,14 +88,17 @@
 blocks.
 
 $matrix
 
-Chains scoring below a threshold were discarded; the remaining
-chains are displayed in this track.</P>
+Chains scoring below a minimum score of '$chainMinScore' were discarded;
+the remaining chains are displayed in this track.  The linear gap
+matrix used with axtChain:<BR>
+$chainLinearGap
+</P>
 
 <H3>Net track</H3>
 <P>
-Chains were derived from blastz alignments, using the methods
+Chains were derived from lastz 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. 
@@ -110,9 +113,10 @@
 diverged.</P>
 
 <H2>Credits</H2>
 <P>
-Blastz was developed at <A HREF="http://bio.cse.psu.edu/" 
+Lastz (previously known as 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>