Homework #2 (80 points)

Assigned: 1/13/05 ---> Due: 1/25/05

There are three parts to this homework. You will be generating one document for each part of the homework. The main objective of these tasks is to make sure that you know how to use the tools that might come in handy for your term project or for other analyses you might end up doing in this courese as well as outside of this course. Tutorials are available on line for Gene Inspector and Gene Construction Kit, and extensive help is available at the NCBI web site.

For some of the results you will need to capture part of the screen and paste it into a Word document. On the Mac, use command-shift-4 to select an area of the screen to be saved as a file; on Windows, use Alt-PrintScreen. You can then "place" the file image into your Word document.

Once you have generated the three documents, you will need to create a folder containing those three documents and hand that in electronically (Instructions).

1. Gene Inspector 1.6 - All of the analyses in this section should be handed in as a single GI notebook - name the notebook GI_HW2.nbk. (40 points)

1. Determine the dinucleotide base composition for your unknown sequence and display the results as a graph in a Gene Inspector notebook. If you notice anything interesting in the results, add some comments to the notebook describing what you observe and perhaps even some thoughts on what it means. This is best done by creating a text box using the "T" tool in the notebook.
2. Find all repeated sequences in the DNA that are 15 nucleotides long and have no more than one mismatch. Show the results graphically in the same notebook. If you observe something interesting in the initial analysis, try to follow up on it. Try longer or shorter length repeats with more or fewer mismatches allowed to try and fine tune your initial observations. View the results as a table in addition to as a graphic (double-click on the analysis object in the notebook and then look at the choices in the Object menu that appears). Anything interesting? Comment on your observations either in a separate text box or as part of the background notebook text.
3. Plot the base distribution of your unknown sequence using the default parameters for the analysis. Stretch the plot to be the width of the notebook page to better see the results.
4. Show at least one additional base distribution analysis of your unknown DNA that produces results you find interesting. Try using large windows of 50-500 and look at purine, pyrimidine, or single nucleotide distributions (not just the default G+C content). Describe why the results you show are interesting (what have you observed?). Feel free to speculate on the meaning of your observations.

2. Gene Construction Kit 2.5 (20 points)

1. Using your unknown sequence create a sequence display that includes the following restriction enzyme sites marked - EcoRI, HindIII, HinfI, and BamHI. View this as the actual DNA sequence with restriction sites annotated above the sequence. Capture the screen showing part of this result (see top of this page). Place this screen capture into a Word document; name it GCK_HW2.doc.
2. Using FILE > DELUXE IMPORT > SEARCH GENBANK, search for troponin on the "definition" line of a GenBank record. Limit your search to a maximum number of 10 entries to retrieve. Now import the sequence called HSDJ447F3 using the default import conversions. Capture the screen and paste it into the HW1-GCK.doc document.

What to hand in:

• Place all three homework documents you create into a single folder. The folder should be identified with your name in the format LastName_FirstName_HW2.
• Stuff or zip the folder and hand it in through the drop box in Blackboard for this course.

Instructions for submitting homework.