[BioC] retrieving upstream/intronic sequences using biomaRt

Steffen Durinck durincks at mail.nih.gov
Wed Sep 13 14:25:07 CEST 2006

Hi Shamit,

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

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


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
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
URL: http://home.ccr.cancer.gov/oncology/oncogenomics/

Phone: 301-402-8103
Advanced Technology Center,
8717 Grovemont Circle
Gaithersburg, MD 20877

More information about the Bioconductor mailing list