[BioC] retrieving upstream/intronic sequences using biomaRt

[Henrik Hornshøj Jensen]

Thanks for your help, although I was thinking of a bioconductor package.

Regards,
Henrik
 


-----Oprindelig meddelelse-----
Fra: Krys Kelly [mailto:kak28 at cam.ac.uk] 
Sendt: Tuesday, September 19, 2006 12:35 PM
Til: Henrik Hornshøj Jensen; bioconductor at stat.math.ethz.ch
Emne: RE: [BioC] retrieving upstream/intronic sequences using biomaRt

Hi Henrik,

A package?  The more one looks, the more one finds!  The attached spreadsheet is very much a work in progress and a bit messy and incomplete.
We started it after a very quick review of the literature, so it is also far from comprehensive.  However, it will probably give you more than enough information to get started. 

This review should be helpful:

Tompa et al (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 23(1) 137-144. 

The three 'old-timer' programs that everyone seems to use are AlignACE, Meme and Consensus. And we have also been using Weeder, Sombrero and NestedMica.
Be aware that some of the programs (e.g. AlignACE) can give quite different answers on different runs even with the same parameters. And the different programs can give very different answers. I am aware that a number of people (including ourselves) use several of the programs and take the motifs that turn up in most of the programs for further study.

There are also programs that search for known motifs (e.g. MAST (companion to MEME), MSCAN, SiteSeer). Two well-known databases of Transcription Factor Binding Sites are TRANSFAC and JASPAR.

Hope this helps.

Krys


Dr Krystyna A Kelly
University of Cambridge
Department of Pathology
Molteno Building, Tennis Court Road
Cambridge CB2 1QP
Tel:    01223 333331
Email: kak28 at cam.ac.uk
 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Henrik Hornshøj Jensen
Sent: 19 September 2006 10:33
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] retrieving upstream/intronic sequences using biomaRt

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/

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

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