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I just figure out the way to query UTR sequence from ensembl by biomart tool.
It is very simple compare with using bioperl to parse gbk file to extract UTR sequence.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | require(biomaRt)
require(org.Hs.eg.db)
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
eg <- mappedkeys(org.Hs.egGO)
utr <- getSequence(id=eg, type="entrezgene", seqType="3utr", mart=ensembl)
outfile <- file("human-3utr.fa", "w")
for (i in 1:nrow(utr)) {
h = paste(c(">", utr[i,2]), collapse="")
writeLines(h, outfile)
writeLines(utr[i,1], outfile)
}
close(outfile) |
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