Nothing
#------------------------------------------------------------------------
# Protein coordinates -> Genomic coordinates
# HEXA:
#------------------------------------------------------------------------
# Load functions
require(magrittr)
require(multicrispr)
filter <- ensembldb::filter
UniprotMappingTypeFilter <- ensembldb::UniprotMappingTypeFilter
UniprotDbFilter <- ensembldb::UniprotDbFilter
# Map identifiers: PRNP -> ENST00000379440
ensdb <- multicrispr::EnsDb.Hsapiens.v98()
ensdb %<>% filter(UniprotMappingTypeFilter('DIRECT', condition = "=="))
ensdb %<>% filter(UniprotDbFilter('SWISSPROT', condition = "=="))
ensembldb::columns(ensdb)
mycolumns <- c(
'UNIPROTID', 'PROTEINID', 'TXID',
'SEQCOORDSYSTEM', 'SEQNAME', 'SEQSTRAND',
'GENESEQSTART', 'GENESEQEND',
'TXSEQSTART', 'TXSEQEND', 'TXCDSSEQSTART', 'TXCDSSEQEND',
'PROTEINSEQUENCE')
hexa <- ensembldb::select(ensdb, 'HEXA', mycolumns, 'SYMBOL')
# single ENST / ENSP
# Google helped to locate Tay Sachs locus
gr <- GenomicRanges::GRanges('chr15:72346580-72346583', strand = '-',
seqinfo = seqinfo(bsgenome))
BSgenome::getSeq(bsgenome, gr)
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