Assignment #5:
  1. Page 171 Web Exploration Questions 1-4 (Using the NCBI ORF Finder) It may be helpful to search for "Cloning Vector pACYC184"
  2. Page 172 Web Exploration Questions 5-9 (Using EasyGene)
  3. Use Genemark to predict genes in pACYC184. How do the results compare to EasyGene?
  4. Lets look up some human genomic dna.
    1. Go to the genome browser at UCSC.
    2. Enter the genome browser in the upper left corner (Try this if you cant find it).
    3. Look up the dyrk1a gene on chromosome 21. You can enter it in the "position or search term" window (Try this if you are desperate)
    4. Zoom out 10x so you can see other genes.
    5. In the regulation section at the bottom, turn on CPG Islands.
    6. Which genes near Dyrk1a have CpG islands near the promoter regions?
    7. Select one of the CpG islands. How are CpG islands calculated in this application?
    8. Now grab this region (chr21:37,378,147-38,195,427) by selecting the "DNA" tab at the top of the window. Unselect the repeat mask and "get dna".
    9. Copy the dna to your clipboard for use in another CPG island predictor. (if you got lost, you can use this data
    10. Look for genes using the NCBI ORF finder and EasyGene.
    11. Do CpG islands help you to identify which ORFs correspond to genes? (you can use the EMBOSS tool to find CpG islands).
  5. Use the perl script ch6onown.pl in ~clement/cs418/ch6 to calculate the CpG islands in the Dyrk1a data. Plot the output using excel or some other package and attach it to your assignment.