Homework #3 (130 points)

Assigned: 1/31/08 ---> Due: 2/7/08

There are three parts to this homework. All the sequences you need are in the zipped GI sequence files here. You can copy and paste some of these sequences for use in the Web analyses. If you cannot access the HW3 GI sequences file for some reason, the actual sequences themselves are available as plain text.

Gene Inspector 110 points

• Look for the coding region in Drosophila HSP70 DNA using TESTCODE. What seems to be the coding region based on the TESTCODE analysis? Save your notebook as GI_HW3.nbk. (10 pts)
• Now run a CodonPreference analysis on the same Drosophila HSP70 DNA using the Drosophila table as well as one other organism's codon preference table. Show both analyses in the GI notebook. Are there any differences? If so, what might be causing these differences? If not, why do you think there aren't any differences - can you back this up with actual data? Type your answers into the notebook. (20 pts)

These tasks pertain to the three coagulation factors (VII, IX, X). We will be trying to assess how similar these sequences are to each other without doing direct sequence comparisons (that's later in the term). Keep all these results in the same GI notebook identified as GI_HW3.nbk.

• Perform hydropathy analyses using different tables and align the results by "stretching" the output objects as necessary. Identify an hyhropathy table that gives the most convincing similarities and state what that table is in the notebook (use a Text Box). (15 pts)
• Perform Prosite Motif searches on the three proteins to identify ALL motifs that occur within the sequences. What sites are similar in each of the three proteins? Comment within the GI notebook. (15 pts)
• In Coagulation Factor IX, find an alpha helical region (of about 20-25 amino acids) and display it as a helical wheel. What does the helical wheel result tell you about the likelihood of this particular helix being in a membrane? (15 pts)
• Design a Gene Inspector table to look for charge distribution in a protein as part of a sliding window analysis. Copy the table you use into the GI notebook (do a screen capture of the table and paste the picture into the notebook) so I can see how you assigned values to each amino acid. Explain how you designed the table. Analyze each of the following using your new table and comment on any patterns that might be found. How might you follow up on any patterns you observe (computationally or biologically)? (35 pts)
  • histones (H2A, H2B, H3)
  • membrane proteins (three different rhodopsins)
  • transcription factors (three different TFIIAs)

Web 20 points

• Using the three different rhodopsin sequences, examine the likely position of any transmembrane segments at the following web sites: TMPred, TMHMMv2
• Copy the web graphic for each of these outputs [hold down the mouse button (Mac) or right-click (Windows) directly on the graphic and choose the appropriate item from the popup menu] and paste it into a new Word document Web_HW3.doc. Comment on any similarities or differences you might see.

What to Hand In