Pattern recognition in genes

Question

[ravihansa82]

Dear friends I need advices and guidance from you. I have set of functionally related genes. i have extracted first intron of such genes. based on the literature i could find there cis-regulatory elements such as TATA box, CAAT box and GC box are there and such elements involve in transcriptional regulation. in this case I would like to find out pattern of above elements in first intron of functionally related genes.

So that I need to know how to I start such pattern recognition part..can any body guide me please....

Answer 1

[Cacau]

MEME might be a good choice

http://meme.nbcr.net/meme/

Answer 2

[oganm]

I assume you know the nucleotide probabilities (sequence logo), if not, just create your own by using known occurrences of the pattern. From that you can just slide a window to see how well a location matches to your regulatory region.

If the size is prone to change, use a markov model to represent the pattern and again, by sliding a window, check for probability.

[ravihansa82]

Thank you friend your comments....dunno whether I am correct or not...dear friend I have set of sequence of first introns. I know first intron is having regulatory motifs as mentioned above. Suppose I have 700 TSP gens now I need to determine whether there is a pattern of such elements in that TSP gene sets. may be individual sequences having different arrangement of such elements and then I need to find that type of pattern presence in all TSP genes ....this the thing I really need to start....any suggestion friend?