9541aea4204c8079ea2e464403f2225f6aa33cfd max Mon Sep 14 07:59:00 2026 -0700 uniprot: show the splice variant track, and filter the CAT alignments Two things that were quietly missing. unipSplice has been built since the pipeline rewrite in #19351 and never had a trackDb stanza - "git log -S unipSplice" on uniprot.ra returns nothing, so it was never wired up rather than deliberately dropped. It holds UniProt's splice variant features, 28962 of them on hg38 and 29195 on hs1, and has been invisible on every assembly for years. Added to uniprot.ra and to the archive/contrib template, which is where the hub-served assemblies get their trackDb. The file exists on the same 131 assemblies as unipDomain.bb, so no stanza points at anything missing. The alignments on a CAT assembly were not being filtered with pslSelect. That filter maps a UniProt accession to the transcripts UniProt cross-references for it, and the README is blunt about how much it matters for protein families with nearly identical transcripts. It understood two kinds of id, Ensembl and RefSeq, and CAT names a transcript after its source gene, so hs1 matched neither and fell through unfiltered. Every row of the CAT bigBed carries the Ensembl transcript it was lifted from, so catSourceTransMap joins on that and UniProt's Ensembl cross-reference does the rest. The mapping had to become one-to-many for this: one Ensembl transcript can name several of ours, both because paralogs are lifted from the same source and because duplicate CAT names were given -dup suffixes earlier. It reproduces those suffixes by walking the bigBed in the same order rather than attaching every paralog to every source, which measured 234903 of 234903 hs1 transcripts mapped, no duplicates, against 330749 for the loose version. For every other gene track the lists hold one element and the behaviour is unchanged, which is checked: a single-valued entry still writes exactly one pair line and still counts a version difference, a multi-valued one writes a line per transcript, and an id we do not have is still skipped so pslSelect -qPass passes it through. refs #38300 diff --git src/hg/utils/otto/uniprot/trackDb.template.txt src/hg/utils/otto/uniprot/trackDb.template.txt index 173f1998fac..6457125e861 100644 --- src/hg/utils/otto/uniprot/trackDb.template.txt +++ src/hg/utils/otto/uniprot/trackDb.template.txt @@ -1,224 +1,235 @@ # this file is used for building the archive track hub, it is template, not the final file. # doUniprot builds the final file. # if you modify this file, make sure that you also modify the original of the native track in trackDb/uniprot.ra track uniprot$VER shortLabel UniProt $VER longLabel UniProt SwissProt/TrEMBL Protein Annotations, release $VER #group genes visibility hide type bigBed 12 + exonNumbers off compositeTrack on allButtonPair on mouseOverField comments urls uniProtId="http://www.uniprot.org/uniprot/$$#section_features" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" itemRgb on #dataVersion /gbdb/$D/uniprot/version.txt hideEmptySubtracks on track unipAliSwissprot$VER shortLabel SwissProt Aln. longLabel UCSC alignment of SwissProt proteins to genome - $VER priority 1 parent uniprot$VER visibility hide type bigPsl bigDataUrl $VER/unipAliSwissprot.bb searchIndex name,acc urls acc="http://www.uniprot.org/uniprot/$$" hgncId="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" labelFields acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt,uniprotName mouseOverField protFullNames itemRgb off color 2,12,120 indelDoubleInsert on indelQueryInsert on baseColorTickColor contrastingColor baseColorUseCds given baseColorDefault genomicCodons showDiffBasesAllScales on track unipAliTrembl$VER shortLabel TrEMBL Aln. longLabel UCSC alignment of TrEMBL proteins to genome - $VER priority 2 parent uniprot$VER visibility dense type bigPsl bigDataUrl $VER/unipAliTrembl.bb searchIndex name,acc urls acc="http://www.uniprot.org/uniprot/$$" hgncId="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" labelFields acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt,uniprotName mouseOverField protFullNames itemRgb off color 0,150,250 indelDoubleInsert on indelQueryInsert on baseColorTickColor contrastingColor baseColorUseCds given baseColorDefault genomicCodons showDiffBasesAllScales on track unipLocSignal$VER shortLabel Signal Peptide longLabel UniProt Signal Peptides - $VER priority 3 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipLocSignal.bb color 255,0,150 itemRgb off filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipLocExtra$VER shortLabel Extracellular longLabel UniProt Extracellular Domain - $VER priority 4 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipLocExtra.bb color 0,150,255 itemRgb off filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipLocTransMemb$VER shortLabel Transmembrane longLabel UniProt Transmembrane Domains - $VER priority 5 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipLocTransMemb.bb color 0,150,0 itemRgb off filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipLocCytopl$VER shortLabel Cytoplasmic longLabel UniProt Cytoplasmic Domains - $VER priority 6 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipLocCytopl.bb color 255,150,0 itemRgb off filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipChain$VER shortLabel Chains longLabel UniProt Mature Protein Products (Polypeptide Chains) - $VER priority 7 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipChain.bb urls uniProtId="http://www.uniprot.org/uniprot/$$#ptm_processing" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipInterest$VER shortLabel Interest longLabel UniProt Regions of Interest - $VER priority 4 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipInterest.bb itemRgb off filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipDomain$VER shortLabel Domains longLabel UniProt Domains - $VER priority 8 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipDomain.bb urls uniProtId="http://www.uniprot.org/uniprot/$$#family_and_domains" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipDisulfBond$VER shortLabel Disulf. Bonds longLabel UniProt Disulfide Bonds - $VER priority 8 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipDisulfBond.bb filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipModif$VER shortLabel AA Modifications longLabel UniProt Amino Acid Modifications - $VER priority 9 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipModif.bb urls uniProtId="http://www.uniprot.org/uniprot/$$#aaMod_section" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipMut$VER shortLabel Mutations longLabel UniProt Amino Acid Mutations - $VER priority 10 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipMut.bb urls uniProtId="http://www.uniprot.org/uniprot/$$#pathology_and_biotech" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" variationId="http://www.uniprot.org/uniprot/$$" track unipStruct$VER shortLabel Structure longLabel UniProt Protein Primary/Secondary Structure Annotations - $VER priority 11 parent uniprot$VER visibility hide type bigBed 12 + bigDataUrl $VER/unipStruct.bb urls uniProtId="http://www.uniprot.org/uniprot/$$#structure" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipOther$VER shortLabel Other Annot. longLabel UniProt Other Annotations - $VER priority 11 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipOther.bb urls uniProtId="http://www.uniprot.org/uniprot/$$#family_and_domains" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipRepeat$VER shortLabel Repeats longLabel UniProt Repeats - $VER priority 12 parent uniprot$VER visibility dense type bigBed 12 + bigDataUrl $VER/unipRepeat.bb urls uniProtId="http://www.uniprot.org/uniprot/$$#family_and_domains" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) track unipConflict$VER shortLabel Seq. Conflicts longLabel UniProt Sequence Conflicts - $VER priority 13 parent uniprot$VER off visibility dense type bigBed 12 + bigDataUrl $VER/unipConflict.bb urls uniProtId="http://www.uniprot.org/uniprot/$$#Sequence_conflict_section" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + track unipSplice$VER + shortLabel Splice Variants + longLabel UniProt Splice Variants - $VER + priority 14 + parent uniprot$VER off + visibility dense + type bigBed 12 + + bigDataUrl $VER/unipSplice.bb + urls uniProtId="http://www.uniprot.org/uniprot/$$#sequences" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + #searchTable unipAliSwissprot #searchType bigBed #searchDescription UniProt/SwissProt manually curated Proteins mapped to the genome by UCSC #searchTable unipAliTrembl #searchType bigBed #searchDescription UniProt/TrEMBL predicted Proteins mapped to the genome by UCSC