src/hg/makeDb/doc/loxAfr3.txt 1.4

Index: src/hg/makeDb/doc/loxAfr3.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/loxAfr3.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/makeDb/doc/loxAfr3.txt	23 Jul 2009 15:14:50 -0000	1.3
+++ src/hg/makeDb/doc/loxAfr3.txt	27 Aug 2009 18:05:07 -0000	1.4
@@ -301,4 +301,24 @@
     featureBits loxAfr3 blastHg18KG xenoRefGene  -enrichment
 # blastHg18KG 1.362%, xenoRefGene 1.615%, both 0.695%, cover 51.03%, enrich 31.60x
     rm -rf blastOut
 #end tblastn
+
+#########################################################################
+# lastz swap from Mouse Mm9 (DONE - 2009-08-27 - Hiram)
+    # original alignment
+    cd /hive/data/genomes/mm9/bed/lastzLoxAfr3.2009-08-12
+    cat fb.mm9.chainLoxAfr3Link.txt
+    #	684326090 bases of 2620346127 (26.116%) in intersection
+
+    mkdir /hive/data/genomes/loxAfr3/bed/blastz.mm9.swap
+    cd /hive/data/genomes/loxAfr3/bed/blastz.mm9.swap
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/mm9/bed/lastzLoxAfr3.2009-08-12/DEF \
+	-swap -noLoadChainSplit -chainMinScore=3000 -chainLinearGap=medium \
+	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+	-syntenicNet > swap.log 2>&1 &
+    #	real    123m9.342s
+    cat fb.loxAfr3.chainMm9Link.txt 
+    #	673856452 bases of 3118565340 (21.608%) in intersection
+
+#########################################################################