[BioC] Motif search

[nooshin]

Thanks for reply.

Answer for the questions:
1) for one TF I have position weight matrix and for the second one I 
have only the sequence.
2) I need both, exact and approximate match
3) Yes, exactly :)

-Nooshin


On 04/20/2012 04:19 PM, Paul Shannon wrote:
>>
>> I'm so new in doing sequence analysis and I have a small project to do, which I need help for.
>> I have a known motif of binding site for one TF in Arabidopsis thaliana and I have to find out if this motif is enriched in 500-bps sequences from a set of genes. I don't know any package or function for this. I would be so thankful if anybody could help me.
>>
> Having recently learned how to do something very similar, I'd be glad to help.  A few clarifying questions:
>
>   1) In what form is the binding site expressed?  Simple sequence, position weight matrix?
>   2) Do you need only exact matches to this motif?  Or approximate matches also?
>   3) I presume you will be looking for matches in the promoters of your set of genes.  True?
>
>   - Paul
>
>> Thanks,
>> Nooshin
>>
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