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

[Ivan Gregoretti]

For motif identification, I have successfully used the cosmo library.

Ivan



On Sun, Oct 23, 2011 at 2:16 PM, Yuan Hao <yuan.x.hao at gmail.com> wrote:
> 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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>
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