Courtney L. Merriam Week 9: Difference between revisions

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==Methods and Results==
==Methods and Results==
===Defining Your HIV Structure Research Project===
#What is your question?
#*
#Make a prediction about the answer to your question before you begin your analysis.
#*
#Which subjects, visits, and clones will you use to answer your question?
#*
#Justify why you chose the subjects, visits, and clones you did.
#*
===HIV Structure In-class Activity===
*Convert your DNA sequences into protein sequences.
*Convert your DNA sequences into protein sequences.
*#How will you do this?
*#How will you do this?
Line 27: Line 37:
*#Explain why you think this.
*#Explain why you think this.
*#*
*#*
*Create a presentation for Week 10 formatted similarly to the past project
*Instead of using Cn3D or StarBiochem to do this, you could use the program ConSurf.


==Data and Files==
==Data and Files==
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==Acknowledgments==
==Acknowledgments==
I collaborated with [[User:|User:]] and [[User:]] in class on this assignment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
I collaborated with [[User:Avery Vernon-Moore|Avery Vernon-Moore]] and [[User:]] in class on this assignment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.


==References==
==References==

Revision as of 12:57, 25 October 2016

Purpose

The purpose of this experiment was to

Methods and Results

Defining Your HIV Structure Research Project

  1. What is your question?
  2. Make a prediction about the answer to your question before you begin your analysis.
  3. Which subjects, visits, and clones will you use to answer your question?
  4. Justify why you chose the subjects, visits, and clones you did.

HIV Structure In-class Activity

  • Convert your DNA sequences into protein sequences.
    1. How will you do this?
    2. How will you know that it was done correctly?
  • Perform a multiple sequence alignment on the protein sequences.
    1. Are there more or fewer differences between the sequences when you look at the DNA sequences versus the protein sequences?
    2. How do you account for this?
  • 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?
    1. How are they applicable?
    • In particular, you should perform the secondary structure prediction on the V3 fragment.
  • Download the structure file for the paper we read in journal club from the NCBI Structure Database.
  • Answer the following:
    1. Find the N-terminus and C-terminus of each polypeptide tertiary structure.
    2. Locate all the secondary structure elements. Do these match the predictions made above?
    3. Locate the V3 region and figure out the location of the sequences from the alignment in the structure.
    4. Analyze whether the amino acid changes that you see in the multiple sequence alignment would affect the 3D structure
    5. Explain why you think this.
  • Instead of using Cn3D or StarBiochem to do this, you could use the program ConSurf.

Data and Files

No files or data was used for this assignment.

Conclusion

Acknowledgments

I collaborated with Avery Vernon-Moore and [[User:]] in class on this assignment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

References

[http://

Useful Links

Courtney L. Merriam

Clas Page: Bioinformatics Laboratory

Weekly Assignments Individual Journal Assignments Shared Journal Assignments
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