The easiest way to get UTR sequence

March 2, 2011
By

(This article was first published on YGC » R, and kindly contributed to R-bloggers)

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.

?View Code RSPLUS
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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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