0831c6df812bb7ed7883c79681e4873a12aeddca lrnassar Mon Aug 2 12:59:14 2021 -0700 Fixing trackDB and turning on uniprot all otto cron refs #27756 diff --git src/hg/makeDb/trackDb/uniprot.alpha.ra src/hg/makeDb/trackDb/uniprot.alpha.ra deleted file mode 100644 index 3e870a4..0000000 --- src/hg/makeDb/trackDb/uniprot.alpha.ra +++ /dev/null @@ -1,226 +0,0 @@ -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/$D/uniprot/version.txt -hideEmptySubtracks on - - track unipAliSwissprot - shortLabel SwissProt Aln. - longLabel UCSC alignment of SwissProt proteins to genome - priority 1 - parent uniprot - visibility hide - type bigPsl - bigDataUrl /gbdb/$D/uniprot/unipAliSwissprot.bb - searchIndex name,acc - urls acc="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 - - 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="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 - - track unipFullSeq - shortLabel UniProt Proteins - longLabel Full UniProt Protein Sequences - priority 3 - parent uniprot - visibility dense - type bigBed 12 + - bigDataUrl /gbdb/$D/uniprot/unipAliSwissprot.bb - color 255,0,150 - itemRgb off - - track unipLocSignal - shortLabel Signal Peptide - longLabel UniProt Signal Peptides - priority 3 - parent uniprot - visibility dense - type bigBed 12 + - bigDataUrl /gbdb/$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 SwissProt Proteins mapped to the genome by UCSC - -searchTable unipAliTrembl -searchType bigBed -searchDescription TrEMBL Proteins mapped to the genome by UCSC