How to find motif frequencies

[asankaf]

Hi,

I am new to molecular biology and I am going to cluster yeast gene using seceral data sources. I know that gene can be clustered using gene expression data and using other alternatives. I klnow that motif frequencies is also a nother solution. I have read in a paper that using frequency measure of motifs we can cluster genes.
Can anyone tell me how to find motif frequencies for a geven gene.
for ex: how to find frequency motif for gene STU2 (from yeast genome)

Thanks a lot in advance,
Asanka.

[zami'87.]

I dont have enough experience to give lab advices..but you could use hydropathy plot for determing hydrophilic and hydrophobic parts of protein thus predicting its conformation