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/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 306dfdbd6aa..23391b5776a 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -642,15 +642,33 @@ hg38 epigenCentral epicV2illuminaMethylation Array probes that include every CpG site in this track hg38 epicV2illuminaMethylation epigenCentral CpG probes of this array that are part of curated DNA methylation episignatures hg38 epigenCentral snpArrayIllumina850k Array probes that include nearly all CpG sites in this track hg38 snpArrayIllumina850k epigenCentral CpG probes of this array that are part of curated DNA methylation episignatures hg19 constraintSuper predictionScoresSuper Per-variant deleteriousness and pathogenicity scores, rather than regional constraint hg19 predictionScoresSuper constraintSuper Regional and gene-level constraint measured from population variation hg19 ~jarvis ukbDepletion Another score for how depleted of variation a non-coding region is hg19 ~hmc gnomadPLI Another constraint metric derived from the absence of variation in population data hg19 hmc ucscGenePfam The Pfam domains that homologous missense constraint is calculated over hg19 ucscGenePfam hmc Missense constraint measured across homologous positions within these domains # mm10 mouse strain cross-links: mm10 mm10Strains1 mouseStrainsCactus Whole-genome alignment of the 16 strain assemblies to the reference mm10 mouseStrainsCactus mm10Strains1 Alternate strain sequences mapped to their reference genome location + +# GPN-Star: +hg38 gpnStarLogoV cons100way Conservation scores from the same 100-vertebrate alignment +hg38 cons100way gpnStarLogoV A genomic language model trained on this alignment +hg38 gpnStarLogoM cons447way Conservation scores from the same 447-mammal alignment +hg38 cons447way gpnStarLogoM A genomic language model trained on this alignment +hg38 gpnStarLogoP cons447way Primate conservation scores from the same alignment +hg38 cons447way gpnStarLogoP A genomic language model trained on the primates of this alignment +hg38 gpnStarLogoM constraintSuper Regional constraint scores +hg38 constraintSuper gpnStarLogoM Per-base constraint predicted from whole-genome alignments +mm39 gpnStarLogo cons35way Conservation scores from the same alignment +mm39 cons35way gpnStarLogo A genomic language model trained on this alignment +galGal6 gpnStarLogo cons77way Conservation scores from the same alignment +galGal6 cons77way gpnStarLogo A genomic language model trained on this alignment +dm6 gpnStarLogo cons124way Conservation scores from the same alignment +dm6 cons124way gpnStarLogo A genomic language model trained on this alignment +ce11 gpnStarLogo cons135way Conservation scores from the same alignment +ce11 cons135way gpnStarLogo A genomic language model trained on this alignment