src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.2
1.2 2009/12/08 23:44:45 hiram
adding chainNetRn4 and chainNetHg18 for Cow bosTau browsers and setting appropriate release tags to separate from older individual tracks
Index: src/hg/makeDb/trackDb/trackDb.chainNet.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.chainNet.ra,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/makeDb/trackDb/trackDb.chainNet.ra 7 Dec 2009 22:00:51 -0000 1.1
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra 8 Dec 2009 23:44:45 -0000 1.2
@@ -1,559 +1,641 @@
# "$Id$";
# release alpha until individual fr2 tracks are obsolete
track chainNetFr2
release alpha
compositeTrack on
shortLabel Fugu Chain/Net
longLabel Fugu (Oct. 2004/fr2), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 159
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
matrixHeader A, C, G, T
otherDb fr2
chainMinScore 5000
chainLinearGap loose
spectrum on
html chainNet
track chainFr2
release alpha
subTrack chainNetFr2
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain fr2
track netFr2
release alpha
subTrack chainNetFr2
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign fr2 chainFr2
track chainNetTetNig2
compositeTrack on
shortLabel Tetraodon Chain/Net
longLabel Tetraodon (Mar. 2007/tetNig2), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 159
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
matrixHeader A, C, G, T
otherDb tetNig2
chainMinScore 5000
chainLinearGap loose
spectrum on
html chainNet
track chainTetNig2
subTrack chainNetTetNig2
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain tetNig2
track netTetNig2
subTrack chainNetTetNig2
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign tetNig2 chainTetNig2
track chainNetDanRer6
compositeTrack on
shortLabel Zebrafish Chain/Net
longLabel Zebrafish (Dec. 2008/danRer6), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 159
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
matrixHeader A, C, G, T
otherDb danRer6
chainMinScore 5000
chainLinearGap loose
spectrum on
html chainNet
track chainDanRer6
subTrack chainNetDanRer6
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain danRer6
track netDanRer6
subTrack chainNetDanRer6
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign danRer6 chainDanRer6
# release alpha until individual oryLat2 tracks are obsolete
track chainNetOryLat2
release alpha
compositeTrack on
shortLabel Medaka Chain/Net
longLabel Medaka (Oct. 2005/oryLat2), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 165.5
color 100,50,0
altColor 255,240,200
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
matrixHeader A, C, G, T
otherDb hg19
chainMinScore 3000
chainLinearGap medium
html chainNet
track chainOryLat2
release alpha
subTrack chainNetOryLat2
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain oryLat2
otherDb oryLat2
track netOryLat2
release alpha
subTrack chainNetOryLat2
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign oryLat2 chainOryLat2
otherDb oryLat2
# release alpha until individual gasAcu1 tracks are obsolete
track chainNetGasAcu1
compositeTrack on
shortLabel Stickleback Chain/Net
longLabel Stickleback (Feb 2006/gasAcu1), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 181
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
matrixHeader A, C, G, T
otherDb gasAcu1
chainMinScore 3000
chainLinearGap medium
spectrum on
html chainNet
release alpha
track chainGasAcu1
release alpha
subTrack chainNetGasAcu1
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain gasAcu1
track netGasAcu1
release alpha
subTrack chainNetGasAcu1
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign gasAcu1 chainGasAcu1
# release alpha until individual galGal3 tracks are obsolete
track chainNetGalGal3
compositeTrack on
shortLabel Chicken Chain/Net
longLabel Chicken (May 2006/galGal3), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 181
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
matrixHeader A, C, G, T
otherDb galGal3
chainMinScore 3000
chainLinearGap medium
spectrum on
html chainNet
release alpha
track chainGalGal3
release alpha
subTrack chainNetGalGal3
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain galGal3
track netGalGal3
release alpha
subTrack chainNetGalGal3
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign galGal3 chainGalGal3
# release alpha until ornAna1 individual chain/net tracks phased out
track chainNetOrnAna1
compositeTrack on
shortLabel Platypus Chain/Net
longLabel Platypus (Mar. 2007/ornAna1), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 191
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
matrixHeader A, C, G, T
otherDb ornAna1
chainMinScore 3000
chainLinearGap medium
spectrum on
html chainNet
release alpha
track chainOrnAna1
release alpha
subTrack chainNetOrnAna1
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain ornAna1
track netOrnAna1
release alpha
subTrack chainNetOrnAna1
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign ornAna1 chainOrnAna1
track chainNetMonDom5
compositeTrack on
shortLabel Opossum Chain/Net
longLabel Opossum (Oct. 2006/monDom5), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 191
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
matrixHeader A, C, G, T
otherDb monDom5
chainMinScore 3000
chainLinearGap medium
spectrum on
html chainNet
track chainMonDom5
subTrack chainNetMonDom5
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain monDom5
track netMonDom5
subTrack chainNetMonDom5
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign monDom5 chainMonDom5
# release alpha until mm9 individual chain/net tracks phased out
track chainNetMm9
compositeTrack on
shortLabel Mouse Chain/Net
longLabel Mouse (Jul. 2007/mm9), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 209
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
matrixHeader A, C, G, T
otherDb mm9
chainMinScore 3000
chainLinearGap medium
spectrum on
html chainNet
release alpha
track chainMm9
release alpha
subTrack chainNetMm9
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain mm9
track netMm9
release alpha
subTrack chainNetMm9
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign mm9 chainMm9
+# release alpha until rn4 individual chain/net tracks phased out
+track chainNetRn4
+release alpha
+compositeTrack on
+shortLabel Rat Chain/Net
+longLabel Rat (Nov. 2004/rn4), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 209
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb rn4
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+ track chainRn4
+ release alpha
+ subTrack chainNetRn4
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain rn4
+
+ track netRn4
+ release alpha
+ subTrack chainNetRn4
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign rn4 chainRn4
+
track chainNetEquCab2
compositeTrack on
shortLabel Horse Chain/Net
longLabel Horse (Sep. 2007/equCab2), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 240
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
matrixHeader A, C, G, T
otherDb equCab2
chainMinScore 3000
chainLinearGap medium
spectrum on
html chainNet
track chainEquCab2
subTrack chainNetEquCab2
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain equCab2
track netEquCab2
subTrack chainNetEquCab2
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign equCab2 chainEquCab2
# release alpha until canFam2 individual tracks phased out
track chainNetCanFam2
compositeTrack on
shortLabel Dog Chain/Net
longLabel Dog (May 2005/canFam2), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 240
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
matrixHeader A, C, G, T
otherDb canFam2
chainMinScore 3000
chainLinearGap medium
spectrum on
html chainNet
release alpha
track chainCanFam2
release alpha
subTrack chainNetCanFam2
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain canFam2
track netCanFam2
release alpha
subTrack chainNetCanFam2
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign canFam2 chainCanFam2
track chainNetVenter
compositeTrack on
shortLabel Venter Chain/Net
longLabel J. Craig Venter Chain and Net Alignments
subGroup1 view Views chain=Chains net=Nets
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 500
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
track chainVenter1
subTrack chainNetVenter off
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
color 100,50,0
altColor 255,240,200
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
matrixHeader A, C, G, T
type chain venter1
otherDb venter1
track netVenter1
subTrack chainNetVenter off
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign venter1 chainVenter1
otherDb venter1
+track chainNetHg18
+release alpha
+compositeTrack on
+shortLabel Human Chain/Net
+longLabel Human (Mar. 2006/hg18), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 498
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
+matrixHeader A, C, G, T
+otherDb hg18
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+ track chainHg18
+ release alpha
+ subTrack chainNetHg18
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain hg18
+
+ track netHg18
+ release alpha
+ subTrack chainNetHg18
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment net
+ type netAlign hg18 chainHg18
+
track chainNetHg19
compositeTrack on
shortLabel Human Chain/Net
longLabel Human (Feb. 2009/hg19), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 498
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
matrixHeader A, C, G, T
otherDb hg19
chainMinScore 3000
chainLinearGap medium
html chainNet
track chainHg19
subTrack chainNetHg19
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain hg19
track netHg19
subTrack chainNetHg19
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment net
type netAlign hg19 chainHg19
track chainNetPoodle
compositeTrack on
shortLabel Poodle Chain/Net
longLabel Poodle Chain and Net Alignments
subGroup1 view Views chain=Chains net=Nets
dragAndDrop subTracks
visibility hide
visibilityViewDefaults chain=pack net=dense
group compGeno
noInherit on
priority 500
color 0,0,0
altColor 255,255,0
type bed 3
settingsByView chain:spectrum=on
sortOrder view=+
track chainCanFamPoodle1
subTrack chainNetPoodle off
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
color 100,50,0
altColor 255,240,200
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
matrixHeader A, C, G, T
type chain canFamPoodle1
otherDb canFamPoodle1
track netCanFamPoodle1
subTrack chainNetPoodle off
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign canFamPoodle1 chainCanFamPoodle1
otherDb canFamPoodle1