[BioC] Motif search

[Paul Shannon]

> 
> 
> 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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