[BioC] retrieving upstream/intronic sequences using biomaRt

[Steffen Durinck]

No, I don't think there is a package to find motifs in the current 
repository. 
It would be nice to have one.

best,
Steffen

Henrik Hornshøj Jensen wrote:
> 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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>>     
>
>
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