The easiest way to get UTR sequence

Posted by ygc on March 2, 2011 Leave a comment (2) Go to comments

I just figure out the way to query UTR sequences from ensembl by biomart tool.

It is very simple compared with using bioperl to parse gbk files to extract UTR sequences.

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)