53ab3f1e293a91ddf71ec7568f4a6ff827bcd278
lrnassar
  Fri Oct 2 13:52:36 2026 -0700
Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451

diff --git src/hg/makeDb/trackDb/mouse/mm39/gpnStar.ra src/hg/makeDb/trackDb/mouse/mm39/gpnStar.ra
new file mode 100644
index 00000000000..362f8defb91
--- /dev/null
+++ src/hg/makeDb/trackDb/mouse/mm39/gpnStar.ra
@@ -0,0 +1,125 @@
+track gpnStar
+shortLabel GPN-Star
+longLabel GPN-Star genomic language model constraint scores (35 vertebrates)
+superTrack on
+pennantIcon New red ../goldenPath/newsarch.html#TBD "Released TBD"
+dataVersion GPN-Star scores, Hugging Face revision 47e7f05 (September 2026)
+group compGeno
+
+track gpnStarLogo
+shortLabel GPN-Star Logo
+longLabel GPN-Star (35 vertebrates) sequence logo of predicted constraint
+parent gpnStar
+container multiWig
+html gpnStar
+maxWindowToDraw 10000000
+mouseOverFunction noAverage
+dataVersion GPN-Star scores, Hugging Face revision 47e7f05 (September 2026)
+type bigWig 0 2
+aggregate stacked
+logo on
+showSubtrackColorOnUi on
+autoScale off
+viewLimits 0:2
+viewLimitsMax 0:2
+maxHeightPixels 100:40:16
+visibility full
+
+    track gpnStarLogoA
+    shortLabel A
+    longLabel GPN-Star (35 vertebrates) logo height of A
+    parent gpnStarLogo
+    type bigWig 0 2
+    bigDataUrl /gbdb/mm39/gpnStar/A.bw
+    color 0,128,0
+    priority 1
+
+    track gpnStarLogoC
+    shortLabel C
+    longLabel GPN-Star (35 vertebrates) logo height of C
+    parent gpnStarLogo
+    type bigWig 0 2
+    bigDataUrl /gbdb/mm39/gpnStar/C.bw
+    color 0,0,255
+    priority 2
+
+    track gpnStarLogoG
+    shortLabel G
+    longLabel GPN-Star (35 vertebrates) logo height of G
+    parent gpnStarLogo
+    type bigWig 0 2
+    bigDataUrl /gbdb/mm39/gpnStar/G.bw
+    color 255,166,0
+    priority 3
+
+    track gpnStarLogoT
+    shortLabel T
+    longLabel GPN-Star (35 vertebrates) logo height of T
+    parent gpnStarLogo
+    type bigWig 0 2
+    bigDataUrl /gbdb/mm39/gpnStar/T.bw
+    color 255,0,0
+    priority 4
+
+track gpnStarLlr
+shortLabel GPN-Star -LLR
+longLabel GPN-Star (35 vertebrates) -LLR per alternate allele
+parent gpnStar
+compositeTrack on
+html gpnStar
+maxWindowToDraw 10000000
+mouseOverFunction noAverage
+dataVersion GPN-Star scores, Hugging Face revision 47e7f05 (September 2026)
+type bigWig
+autoScale off
+alwaysZero on
+viewLimits -3:10
+viewLimitsMax -16:16
+negateValues on
+yLineOnOff on
+yLineMark 0
+graphTypeDefault bar
+maxHeightPixels 100:16:16
+windowingFunction mean+whiskers
+visibility dense
+
+    track gpnStarLlrA
+    shortLabel Mutation: A
+    longLabel GPN-Star (35 vertebrates) -LLR: Mutation is A
+    parent gpnStarLlr on
+    type bigWig
+    bigDataUrl /gbdb/mm39/gpnStar/llr_A.bw
+    color 140,60,60
+    altColor 60,60,140
+    priority 1
+
+    track gpnStarLlrC
+    shortLabel Mutation: C
+    longLabel GPN-Star (35 vertebrates) -LLR: Mutation is C
+    parent gpnStarLlr on
+    type bigWig
+    bigDataUrl /gbdb/mm39/gpnStar/llr_C.bw
+    color 140,60,60
+    altColor 60,60,140
+    priority 2
+
+    track gpnStarLlrG
+    shortLabel Mutation: G
+    longLabel GPN-Star (35 vertebrates) -LLR: Mutation is G
+    parent gpnStarLlr on
+    type bigWig
+    bigDataUrl /gbdb/mm39/gpnStar/llr_G.bw
+    color 140,60,60
+    altColor 60,60,140
+    priority 3
+
+    track gpnStarLlrT
+    shortLabel Mutation: T
+    longLabel GPN-Star (35 vertebrates) -LLR: Mutation is T
+    parent gpnStarLlr on
+    type bigWig
+    bigDataUrl /gbdb/mm39/gpnStar/llr_T.bw
+    color 140,60,60
+    altColor 60,60,140
+    priority 4
+