BIOL368/F14:Week 9

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, October 29 at midnight PDT (Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Individual Journal Assignment

  • Store this journal entry as "username Week 9" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL368/F14" category to the end of your wiki page.

HIV Structure Project

To answer your question posed in the Week 8 Assignment, you will need to do the following:

  1. Convert your DNA sequences into protein sequences.
    • How will you do this? And how will you know that it was done correctly?
    • Alternately, you can obtain the protein sequences from the BEDROCK HIV Problem Space.
  2. Perform a multiple sequence alignment on the protein sequences.
    • Are there more or fewer differences between the sequences when you look at the DNA sequences versus the protein sequences?
    • How do you account for this?
  3. Which of the procedures from the Week 8 Assignment that you ran on the entire gp120 sequence are applicable to the V3 fragment you are working with now?
    • How are they applicable?
    • In particular, you should perform the secondary structure prediction on the V3 fragment.
  4. Download the structure file for the paper we read in journal club from the NCBI Structure Database.
  5. These files can be opened with the Cn3D software site that is installed on the computers in the lab (this software is free, so you can download it and use it at home, too.) Alternately, you may choose to use the Star Biochem program to do this portion of your work. Answer the following:
    • Find the N-terminus and C-terminus of each polypeptide tertiary structure.
    • Locate all the secondary structure elements. Do these match the predictions you made above?
    • Locate the V3 region and figure out the location of the sequences from your alignment in the structure.
  6. Once you have oriented yourself, analyze whether the amino acid changes that you see in the multiple sequence alignment would affect the 3D structure and explain why you think this.
    • Instead of using Cn3D or StarBiochem to do this, you could use the program ConSurf.
  7. Your presentation for Week 10 will be formatted similarly to the previous HIV Evolution Project. In this case, you will want to work on creating structure figures that illustrate what result you are trying to show.
    • Your presentation will be 15-30 minutes long (shorter for individual presentations, longer for group presentations; approximately 15-30 slides, one per minute). Include:
      • Title slide
      • Outline slide
      • Background that led you to ask your research question
      • Your question
      • How you answered your question, method/results
      • Interpretation of your results; answer to your question
    • Upload your slides to the OpenWetware wiki by the Week 9 journal assignment deadline. You may make changes to your slides in advance of your presentation, but you will be graded on what you upload by the journal deadline.

Note: The individual journal entry for this week is worth 10 points like all other journal entries. The research presentation is worth 70 points.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F14:Class Journal Week 9 page. If this page does not exist yet, go ahead and create it.
  • Link to the shared journal entry from your user page; this should be part of your template.
  • Link the shared journal page to this assignment page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL368/F14" category to the end of the wiki page (if someone has not already done so).


  1. Which project was more interesting to you: studying the evolution of the HIV virus or studying the structure → function relationship? Why?
    • Note that I'm not asking about the tools you used, but the scientific problem studied.
  2. What was the best part of working with a partner on this project? What was the worst part? Has this changed since your last project? Why or why not?
  3. Besides the scientific conclusion of your project, what have you learned about the process of doing research as a result of this project?