Exercise : Identify regulatory elements in genomic sequences

Objective: identify regulatory elements in the 10-kb 5' non-coding region of  human and mouse IL2R-alpha genes .
 
We will use the CONSITE web server (NB: CONSITE uses the JASPAR database of transcription factor binding sites profiles)

Step 1: Identify potential transcription factor binding sites  by analysing single sequences

    - search for all putative TF binding sites
    - try with or without specifity threshold

Step 2: Identify conserved potential transcription factor binding sites by analysing orthologous pairs of sequences

NB: some regulatory sites have been experimentally characterized in human IL2-Ra gene.

Step 3: Search for CpG island promoters with CpGProD

For review, see:

	Wasserman WW, Sandelin A.	Related Articles, Links
	Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 2004 Apr;5(4):276-87.