Assignment 7. Discoverying Regulatory Elements
In this assignment you will use some of the programs at Jacques Van Helden's website (http://rsat.ulb.ac.be/rsat/) to discover regulatory elements.

1. For the genes, download the 800 upstream region (select -800 to -1) for the genes in the MET family. Gene names are entered 1 per line. The organism is Saccharomyces cerevisiae (yeast). Here are the names:
   MET3 MET2 MET14 MET6 SAM1 SAM2 MET1 MET30 MUP3
2. Use ogligo-analysis with size 6 and report the significant elements that you found. Do not present all the results of the analysis.
3. Repeat the last question, but this time select Markov-Model of order 2 as the background model. If you get no answers, can you explain why. If it finds anything, does it correspond to anything found previously.
4. Repeat the last question but this time select Markov-Model of order 3 as the background model.
5. On the same file, run Gibbs sampling and report the top pwm. Compute and report the consensus sequence corresponding to this matrix. Does it match with any regulatory elements that you found by other search methods?