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/trackDb.ra src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
index 67a486901a4..4522bc07ca0 100644
--- src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
+++ src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
@@ -1,75 +1,77 @@
 include mouseDevTimecourse.ra
 
 # Local declaration so that local gold.html is picked up.
 track gold override
 html gold
 
 # Local declaration so that local gap.html is picked up.
 track gap override
 html gap
 
 #track chainNetCalJac4 override
 #chainMinScore 3000
 
 #track ensGene override
 #priority 2.02
 
 track xenoRefGene override
 visibility hide
 #priority 2.03
 
 track mrna override
 priority 2.1
 
 searchTable gold
 shortCircuit 1
 termRegex [ABCFLM][ACEFGHLNOPQRTUXY][AEKJQR0-9]+(\.[0-9_]+)?
 query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
 searchPriority 8
 
 #include evaSnp.ra
 include xenoRefGene.ra
 include trackDb.35way.ra
 include trackDb.chainNet.ra
 include trackDb.syntenicNet.ra alpha
 include trackDb.rbestNet.ra alpha
 include trackDb.gencode.ra
 include knownGene.ra
 include knownGeneArchive.ra
 include reMap.ra
 
 include liftOverMm10.ra
 
 track vistaEnhancersBb
 shortLabel VISTA Enhancers
 longLabel VISTA Enhancers
 group regulation
 url https://enhancer.lbl.gov/vista/element?vistaId=$$
 type bigBed 9 +
 mouseOverField patternExpression
 urlLabel View on the VISTA Enhancer Browser
 bigDataUrl /gbdb/mm39/vistaEnhancers/vistaEnhancers.bb
 itemRgb on
 
 include ../refSeqComposite.mm10.mm39.ra
 
 include cytoBand.ra
 
 track ucscGenePfam override
 shortLabel Pfam in GENCODE
 longLabel Pfam Domains in GENCODE Genes
 html gencodePfam
 
 include vgp577way.trackDb.ra alpha
 
 include tad.ra alpha
 
 track dnaMethylation
 superTrack on
 shortLabel DNA Methylation
 longLabel DNA Methylation
 group regulation
 priority 3
 html dnaMethylation.html
 
 include methbase2.ra alpha
+
+include gpnStar.ra alpha