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 sequences from ensembl by biomart tool.

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

?View Code RSPLUS
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)

Related Posts

To leave a comment for the author, please follow the link and comment on his blog: YGC » R.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...



If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Tags: , , ,

Comments are closed.