gene clustering using motif

[asankaf]

Hi,

I am new to molecular biology and I am going to cluster yeast gene using several 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. how can i use motif to 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.

[ljxue]

Firstly, a list of motifs should be obtained from some databases containing transcription factor binding site. Or you can get the motifs from your data using tools such as MEME,
Then map the elements onto your sequences using Patscan and so on.
Then summarize the number of sites.

[asankaf]

thanks a lot for your suggestions.
here I only know the gene name. how can I find a sequence for a given gene.
to find motif ,what sequence we use? DNA(in terms of A,T,C,G) or PROTIEN?

[ljxue]

I do not work on yeast, you can try the page

http://www.yeastgenome.org/cgi-bin/seqTools

Mostly,regulatin motifs refers to the cis-elements of the gene promoters.
The method I said it not for green hand.You can ask others good at
bioinformatics to help you to deal with your data.

If you want to cluster genes using the seqences of CDS,cDNA, or protein
you can simplely use MEGA. Your can also find these sequences
in http://www.yeastgenome.org