Find binding sites for transcription factor in a sequence

[turnersd]

I want to look at the promoter sequence of human IgM (ENSG00000162897), which I can easily retrieve with biomart. I'm specifically looking for potential binding sites for transcription factors called E-proteins which bind to the consensus sequence CANNTG. What's the easiest way to do this?

Thanks.

[rmflight]

biostrings matchpattern

The Bioconductor package Biostrings has a function "matchPattern" for looking for exact matches, and "matchPWM" for looking for patterns based on position weight matrices. This should probably do what you want.

[SNPsaurus]

turnersd, that particular motif will be found everywhere (every 100-400 bp). You might want to take hits and correlate them with evolutionary conservation at the UCSC browser, and bring in other genomic data used to find enhancer sequences (look at the ENCODE project articles that came out a bit ago, for example).

[p.j]

i have to develop a statistical machine learning tool for microarray gene expression data.

to develop gene networks