The easiest way to get UTR sequence

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.

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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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Tags: BioC, English, Genomics, R