ASSIGNMENTS

KineMage exercise

• Download the KineMage software for Windows or MAC
. If you need extra instructions read the Installation guide.
• Search and download any KineMage file (suffix kin) using the Protein Science gopher server
• Run KineMage in your PC or MAC and open the kin file you downloaded.

• Turn on and off the buttons that activate parts of the active site and other parts of the protein.

Sequence Analysis exercise:

Information to gather while you are completing the second exercise:



• the name of the gene used in the exercise
  
• the full nucleic acid sequence
  
• the full protein sequence
  
• a list of enzymes that do not cut the nucleic acid sequence
  
• Based on the Transmembrane prediction, do you think this protein is a transmembrane protein ?
• COLLECT THE ANSWERS FROM THE FOLLOWING EXERCISES AND E-MAIL THEM TO cascio@ucla.edu

WARNING: THE BLAST SERVER AT NCBI IS WORKING AT 50% CAPACITY. EXPECT A 5 TO 10 MINUTES DELAY FOR EACH SEARCH.

1. Perform a blast search at BCM using the following sequence:
   CCCGGGGATG GCTCCGTGGC CTCACGAGAA CAGCTCTCTT GCCCCATGGC CGGACCTCCC
   (Highlight the sequence, then choose copy from the Edit menu. Go to the Blast search page and Edit, Paste the sequence into the sequence box)
   
2. Click on the R icon next to the first aligned sequence to fetch the sequence of the gene.
   
3. Copy the gene sequence (and only the gene sequence, no words or other stuff) to the clipboard (Edit, copy - just like before).
   
4. Go to the Sequence Utility of the BCM launcher and perform a Webcutter restriction enzyme search. (Edit, Paste the sequence into the sequence box) At the bottom of the Webcutter results you will find a list of restriction enzymes that WILL NOT cut the sequence.
   
5. Go back to the Sequence Utilities page (click back) and perform a six reading frame translation using the same sequence.
   
6. Copy the most likely protein translation (in this case the correct reading frame is the one with ONLY ONE asterisk -*- ) to the clipboard.
   
7. Go to the Secondary Structure Prediction Section and perform a Tmpred search.