1a36012f9f2eb9d087e503b1fd2c37f3a9adedfd max Fri Nov 26 08:11:01 2021 -0800 A major update for the UniProt otto job, refs #28560 diff --git src/hg/makeDb/trackDb/uniprot.ra src/hg/makeDb/trackDb/uniprot.ra new file mode 100644 index 0000000..58991df --- /dev/null +++ src/hg/makeDb/trackDb/uniprot.ra @@ -0,0 +1,226 @@ +# if you modify this file, make sure that you also modify /hive/data/outside/otto/uniprot/uniprot.ra +# which is the template for the hub in the archive/ on hgdownload. This hub is build for every release, +# so users can open old versions of UniProt + +track uniprot +shortLabel UniProt +longLabel UniProt SwissProt/TrEMBL Protein Annotations +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/$D/uniprot/version.txt +html uniprotAlpha.html +hideEmptySubtracks on + + track unipAliSwissprot + shortLabel SwissProt Aln. + longLabel UCSC alignment of SwissProt proteins to genome + priority 1 + parent uniprot + visibility hide + type bigPsl + bigDataUrl /gbdb/$D/uniprot/unipAliSwissprot.bb + searchIndex name,acc + urls acc="https://www.uniprot.org/uniprot/$$" hgncId="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" refSeq="https://www.ncbi.nlm.nih.gov/nuccore/$$" refSeqProt="https://www.ncbi.nlm.nih.gov/protein/$$" ncbiGene="https://www.ncbi.nlm.nih.gov/gene/$$" entrezGene="https://www.ncbi.nlm.nih.gov/gene/$$" ensGene="https://www.ensembl.org/Gene/Summary?g=$$" + labelFields name,acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt + mouseOverField protFullNames + itemRgb off + color 2,12,120 + indelDoubleInsert on + indelQueryInsert on + baseColorTickColor contrastingColor + baseColorUseCds given + baseColorDefault genomicCodons + showDiffBasesAllScales on + + track unipAliTrembl + shortLabel TrEMBL Aln. + longLabel UCSC alignment of TrEMBL proteins to genome + priority 2 + parent uniprot off + visibility hide + type bigPsl + bigDataUrl /gbdb/$D/uniprot/unipAliTrembl.bb + searchIndex name,acc + urls acc="https://www.uniprot.org/uniprot/$$" hgncId="https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" refseq="https://www.ncbi.nlm.nih.gov/nuccore/$$" refSeqProt="https://www.ncbi.nlm.nih.gov/protein/$$" ncbiGene="https://www.ncbi.nlm.nih.gov/gene/$$" entrezGene="https://www.ncbi.nlm.nih.gov/gene/$$" ensGene="https://www.ensembl.org/Gene/Summary?g=$$" + labelFields name,acc,uniprotName,geneName,hgncSym,refSeq,refSeqProt,ensProt + mouseOverField protFullNames + itemRgb off + color 0,150,250 + indelDoubleInsert on + indelQueryInsert on + baseColorTickColor contrastingColor + baseColorUseCds given + baseColorDefault genomicCodons + showDiffBasesAllScales on + + track unipLocSignal + shortLabel Signal Peptide + longLabel UniProt Signal Peptides + priority 3 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/unipLocSignal.bb + color 255,0,150 + itemRgb off + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + + track unipLocExtra + shortLabel Extracellular + longLabel UniProt Extracellular Domain + priority 4 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/unipLocExtra.bb + color 0,150,255 + itemRgb off + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + + track unipLocTransMemb + shortLabel Transmembrane + longLabel UniProt Transmembrane Domains + priority 5 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/unipLocTransMemb.bb + color 0,150,0 + itemRgb off + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + + track unipLocCytopl + shortLabel Cytoplasmic + longLabel UniProt Cytoplasmic Domains + priority 6 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/unipLocCytopl.bb + color 255,150,0 + itemRgb off + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + + track unipChain + shortLabel Chains + longLabel UniProt Mature Protein Products (Polypeptide Chains) + priority 7 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/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 + shortLabel Interest + longLabel UniProt Regions of Interest + priority 4 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/unipInterest.bb + itemRgb off + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + + track unipDomain + shortLabel Domains + longLabel UniProt Domains + priority 8 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/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 + shortLabel Disulf. Bonds + longLabel UniProt Disulfide Bonds + priority 8 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/unipDisulfBond.bb + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + + track unipModif + shortLabel AA Modifications + longLabel UniProt Amino Acid Modifications + priority 9 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/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 + shortLabel Mutations + longLabel UniProt Amino Acid Mutations + priority 10 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/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/$$" + + track unipStruct + shortLabel Structure + longLabel UniProt Protein Primary/Secondary Structure Annotations + priority 11 + parent uniprot + group genes + visibility hide + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/unipStruct.bb + urls uniProtId="http://www.uniprot.org/uniprot/$$#structure" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + + track unipOther + shortLabel Other Annot. + longLabel UniProt Other Annotations + priority 11 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/unipOther.bb + urls uniProtId="http://www.uniprot.org/uniprot/$$#family_and_domains" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + + track unipRepeat + shortLabel Repeats + longLabel UniProt Repeats + priority 12 + parent uniprot + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/unipRepeat.bb + urls uniProtId="http://www.uniprot.org/uniprot/$$#family_and_domains" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + + track unipConflict + shortLabel Seq. Conflicts + longLabel UniProt Sequence Conflicts + priority 13 + parent uniprot off + visibility dense + type bigBed 12 + + bigDataUrl /gbdb/$D/uniprot/unipConflict.bb + urls uniProtId="http://www.uniprot.org/uniprot/$$#Sequence_conflict_section" pmids="https://www.ncbi.nlm.nih.gov/pubmed/$$" + filterValues.status Manually reviewed (Swiss-Prot),Unreviewed (TrEMBL) + +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