3d194de4d74f67c1a453035e20c4769d88bec4c4
lrnassar
  Mon Jul 13 12:52:57 2026 -0700
Order popEVE heatmap amino acid rows by class to match the MaveDB track. refs #37791

Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order
(A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the
tracks can be compared row-for-row. Rebuilds popEve.bb; updates the makedoc, the AutoSql
row label comment, and the description page.

diff --git src/hg/makeDb/trackDb/human/popEve.html src/hg/makeDb/trackDb/human/popEve.html
index 0cca151b73c..473d820640a 100644
--- src/hg/makeDb/trackDb/human/popEve.html
+++ src/hg/makeDb/trackDb/human/popEve.html
@@ -4,31 +4,32 @@
 of the variants observed in human populations, yet most have no established clinical
 significance. <a href="https://pop.evemodel.org/" target="_blank">popEVE</a> places missense
 variants on a single, proteome-wide spectrum of
 deleteriousness, so that variants in different genes can be compared directly. It is a deep
 generative model that combines cross-species evolutionary scores with human population
 variation: scores from EVE (an evolutionary variational autoencoder) and the ESM-1v protein
 language model are calibrated against allele observations in the UK Biobank using a Gaussian
 process, yielding a continuous, human-specific measure of variant impact. This track shows
 popEVE scores for single-nucleotide missense substitutions across roughly 18,000 human proteins.
 </p>
 
 <h2>Display Conventions</h2>
 <p>
 Each entry spans one protein at its genomic locus. The heatmap columns correspond to
 individual amino acid positions in the protein, placed at the codon's genomic coordinate.
-The rows correspond to the 20 standard amino acids (A&ndash;Y, alphabetical). Each cell
+The rows correspond to the 20 standard amino acids, ordered by amino acid class to match
+the MaveDB track. Each cell
 shows the popEVE score for substituting the wildtype amino acid at that position with the
 row amino acid. Because popEVE is distributed as a list of genomic single-nucleotide
 variants, only amino acid substitutions reachable by a single-nucleotide change are scored;
 cells for substitutions requiring more than one nucleotide change, for the wildtype amino
 acid, or for positions without a score (for example start codons) are left empty.
 </p>
 
 <p>
 Unlike per-gene scores, popEVE is calibrated across the whole proteome, so cells are colored
 on a single global gradient keyed to the raw popEVE score (lower, more negative scores are
 more deleterious). The color is interpolated between the five anchors below: the published
 severe and moderate thresholds are fixed anchors, and the extremes saturate at the 0.5th and
 99.5th percentiles of the proteome-wide score distribution.
 </p>
 <table style="border-collapse: collapse; border: 1px solid #ccc;">