[BioC] retrieving upstream/intronic sequences using biomaRt

[Henrik Hornshøj Jensen]

Any of you guys know a package that will predict regulatory sites in upstream regions?

Regards,
Henrik
 


-----Oprindelig meddelelse-----
Fra: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] På vegne af Steffen Durinck
Sendt: Wednesday, September 13, 2006 2:25 PM
Til: Shamit Soneji
Cc: BioC
Emne: Re: [BioC] retrieving upstream/intronic sequences using biomaRt

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
URL: http://home.ccr.cancer.gov/oncology/oncogenomics/

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Address:
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