Assignment #5:
- Page 171 Web Exploration Questions 1-4 (Using the NCBI ORF Finder) It may be helpful to search for "Cloning Vector pACYC184"
- Page 172 Web Exploration Questions 5-9 (Using EasyGene)
- Use Genemark to predict genes in pACYC184. How do the results compare to EasyGene?
- Lets look up some human genomic dna.
- Go to the genome browser at UCSC.
- Enter the genome browser in the upper left corner (Try this if you cant find it).
- 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)
- Zoom out 10x so you can see other genes.
- In the regulation section at the bottom, turn on CPG Islands.
- Which genes near Dyrk1a have CpG islands near the promoter regions?
- Select one of the CpG islands. How are CpG islands calculated in this application?
- 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".
- Copy the dna to your clipboard for use in another CPG island predictor. (if you got lost, you can use this data
- Look for genes using the NCBI ORF finder and EasyGene.
- Do CpG islands help you to identify which ORFs correspond to genes? (you can use the EMBOSS tool to find CpG islands).
- 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.