Nothing
# Load functions
require(magrittr)
require(multicrispr)
filter <- ensembldb::filter
UniprotMappingTypeFilter <- ensembldb::UniprotMappingTypeFilter
UniprotDbFilter <- ensembldb::UniprotDbFilter
# Map identifiers: CFTR
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')
cftr <- ensembldb::select(ensdb, 'CFTR', mycolumns, 'SYMBOL')
cftr # Two transcripts
# Two distinct proteins
# ENSP00000003084 gold labeled
ensp <- 'ENSP00000003084'
cftr %<>% extract(.$PROTEINID == ensp, )
cftr$PROTEINSEQUENCE %>% substr(507, 509) # DELTA F 508
gr <- ensembldb::proteinToGenome(
IRanges::IRanges(start=508, end=508) %>% set_names(ensp),
ensdb) %>%
extract2(ensp) %>%
(function(y){seqlevelsStyle(y) <- 'UCSC'; y})
bs <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
BSgenome::getSeq(
bs, seqnames(gr), start = start(gr), end = end(gr), strand = '+')
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.