BIOL368/F11:Week 8

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** Don't forget to add the "BIOL368/F11" category to the end of your wiki page.
** Don't forget to add the "BIOL368/F11" category to the end of your wiki page.
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=== Working with Protein Sequences In-class Activity ===
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* This week we will begin to learn how to analyze protein structures.  For today, we will be using the ''Bioinformatics for Dummies'' book extensively, so be sure to bring it to class. We will be using some bioinformatics tools to analyze the structure of the gp120 envelope protein.
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* Chapter 2:  Retrieving Protein Sequences/Retrieving a list of Related protein sequences (pp. 42-51 in second edition).  The example worked through in the book uses the sequence of an enzyme called dUTPase.  Follow the book example yourself, but instead of investigating dUTPase, use the HIV gp120 envelope protein instead.
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* Chapter 4: Reading a SWISS-PROT entry (pp. 110-123 in the second edition).  The example worked through in the book is the epidermal growth factor receptor.  Work through this example using the HIV gp120 envelope protein instead.
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* Chapter 5: ORFing your DNA sequence (pp. 146-147 in second edition).  In the previous section of the course, we were working with DNA sequences from the HIV gp120 envelope protein.  Take one of your DNA sequences and follow the instructions to find the open reading frames in the sequence.  Since you were working with just a portion of the entire envelope protein, you may get some strange results.  Compare your results with the SWISS-PROT entry you found for the protein above to decipher what the output means.  Besides the NCBI Open Reading Frame Finder described in the book, ExPASy also has a translation tool you can use, found [http://www.expasy.org/tools/dna.html here].
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* Chapter 6: Working with a single protein sequence (pp. 159-195 in second edition).  Work through the following examples in this chapter using the entire HIV gp120 envelop protein sequence that you obtained from SWISS-PROT.  We will then compare the results of these analyses with the actual structure of the gp120 protein obtained by X-ray crystallography.
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** ProtParam
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** Looking for transmembrane segments
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=== HIV Structure Research Project ===
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* For this project, you can choose to work with the same sequences you used for the [[BIOL368/F11:HIV Evolution | HIV Evolution Project]], or you may choose different sequences.  You will reframe your question from the HIV Evolution Project to make it a structure→function question.  Instead of looking at how the evolution of variation of the viral DNA sequence affects the different patient groups, you will look at how variations in the viral sequence affect the structure and, therefore, function of the virus.  '''''For this week's journal assignment, you must indicate the question that you will study for your project and which data you will use (patients, visits).  Justify your selection of patients and visits. '''''
== Shared Journal Assignment ==
== Shared Journal Assignment ==

Current revision

BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, October 26 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.


Contents

Individual Journal Assignment

  • Store this journal entry as "username Week 8" (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/F11" category to the end of your wiki page.

Working with Protein Sequences In-class Activity

  • This week we will begin to learn how to analyze protein structures. For today, we will be using the Bioinformatics for Dummies book extensively, so be sure to bring it to class. We will be using some bioinformatics tools to analyze the structure of the gp120 envelope protein.
  • Chapter 2: Retrieving Protein Sequences/Retrieving a list of Related protein sequences (pp. 42-51 in second edition). The example worked through in the book uses the sequence of an enzyme called dUTPase. Follow the book example yourself, but instead of investigating dUTPase, use the HIV gp120 envelope protein instead.
  • Chapter 4: Reading a SWISS-PROT entry (pp. 110-123 in the second edition). The example worked through in the book is the epidermal growth factor receptor. Work through this example using the HIV gp120 envelope protein instead.
  • Chapter 5: ORFing your DNA sequence (pp. 146-147 in second edition). In the previous section of the course, we were working with DNA sequences from the HIV gp120 envelope protein. Take one of your DNA sequences and follow the instructions to find the open reading frames in the sequence. Since you were working with just a portion of the entire envelope protein, you may get some strange results. Compare your results with the SWISS-PROT entry you found for the protein above to decipher what the output means. Besides the NCBI Open Reading Frame Finder described in the book, ExPASy also has a translation tool you can use, found here.
  • Chapter 6: Working with a single protein sequence (pp. 159-195 in second edition). Work through the following examples in this chapter using the entire HIV gp120 envelop protein sequence that you obtained from SWISS-PROT. We will then compare the results of these analyses with the actual structure of the gp120 protein obtained by X-ray crystallography.
    • ProtParam
    • Looking for transmembrane segments

HIV Structure Research Project

  • For this project, you can choose to work with the same sequences you used for the HIV Evolution Project, or you may choose different sequences. You will reframe your question from the HIV Evolution Project to make it a structure→function question. Instead of looking at how the evolution of variation of the viral DNA sequence affects the different patient groups, you will look at how variations in the viral sequence affect the structure and, therefore, function of the virus. For this week's journal assignment, you must indicate the question that you will study for your project and which data you will use (patients, visits). Justify your selection of patients and visits.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F11:Class Journal Week 8 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/F11" category to the end of the wiki page (if someone has not already done so).

Reflection

  1. After working with the protein tools on today's assignment, compare your experience with working with the nucleic acid tools versus the protein tools. Which do you like better, and why?
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