[BioC] how to extract promoter regions and detect motif occurrence counts?

[Yuan Hao]

Also, if you are not familiar with R/Bioconductor, UCSC table browser  
may be more straightforward to get promoter sequences, then apply a  
motif searching program over them.

Yuan

On 23 Oct 2011, at 18:22, Steve Lianoglou wrote:

> Hi,
>
> On Sun, Oct 23, 2011 at 12:44 PM, Edward Turner <edtuer at gmail.com>  
> wrote:
>> Hi,
>>
>>  I'm new to bioconductor. Could anyone give some hints which  
>> package(s) I
>> should use for the following purposes:
>>
>> 1. Extract the promoter regions of given 100 genes with Entre ID
>> 2. Count the occurrence of given motif in promoter region of each  
>> gene,
>> respectively.
>
> Get familiar with:
>
> (1) GenomicFeatures
> (2) GenomicRanges
> (3) IRanges
> (4) Biostrings
> (5) The BSgenome.*.* package for the organism you are working with.
>
> (1) You will get the location of promoters using GenomicFeatures,
> which you will define yourself as XX bp upstream from the
> transcription start site of the gene (GenomicFeatures gives you, among
> other things, transcription bounds).
>
> (2) The results from (1) will be returned to you in a data structure
> that is defined in GenomicRanges, which, in turn, are objects that
> rely heavily on the IRanges infrastructure
>
> (3) The biostrings + BSgenome.*.* packages will allow you to find the
> sequences associated with the promoter ranges you defined from (1) and
> look for the occurrence of patterns you are looking for in them.
>
> HTH,
> -steve
>
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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