[BioC] retrieving upstream/intronic sequences using biomaRt

[Steffen Durinck]

Hi Shamit,

Yes, with biomaRt you can get the upstream sequences but currently not 
the intronic sequences.
 Try:

library(biomaRt)
ensmart = useMart("ensembl",dataset="hsapiens_gene_ensembl")
getSequence( id="ENSG00000139618", type="ensembl",mart = ensmart, 
seqType = "5utr")

Cheers,
Steffen


Shamit Soneji wrote:
> Is it possible using biomaRt (or any other R/BioC means) to download the
> upstream and intron sequences for any given ensembl ID?
>
> I know this can be done just using straight biomart, but a facility like
> this from R would be very useful if one wants to search for TF binding
> sites.
>
> Many thanks
>
> Shamit
>
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-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
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