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Pattern recognition in genes

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....

gene
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updated by Ram Ram • written by ravihansa82 ravihansa82

2 answers

MEME might be a good choice

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

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written by Cacau Cacau

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.

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updated by Ram Ram • written by oganm oganm

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?

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updated by Ram Ram • written by ravihansa82 ravihansa82

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