AninditaVarshneya BIOL368 Week 10

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  • Understand more about the gp120 protein structure, and changes in the amino acid sequence. Ultimately, this tells us how the protein structure might affect the function of the protein overall.

Methods and Results

  1. Perform a multiple sequence alignment on the protein sequences that you and your partner are analyzing for your project using the Biology Workbench.
    • Live Data Table
    • Are there more or fewer differences between the sequences when you look at the DNA sequences versus the protein sequences?
      • There were, on average across all visits/clones and all subjects, fewer differences between the DNA sequences than the protein sequences.
    • How do you account for this?
      • I checked the proportion of changes for amino acids and nucleic acids using the formula:
        • % change amino acids = (differences/total number of amino acids)
        • % change nucleic acids = (differences/total number of base pairs)
      • All of this data can be found in the data sheet linked above.


More amino acid changed occurred within each visit for each subject than nucleic acid changes. This data was produced by observing the proportional number of differences between each of the clones at each visit of each subject. In every subject, it was found that proportionally more changes in amino acids occurred than nucleic acid. The later visit (visit 4) had more nonsynonymous mutations as well, as indicated by "no consensus" mutations in the data table. This indicates that over time, more mutations occurred within the DNA that resulted in vastly different amino acids than were originally coded for. This means that the gp120 protein can handle some level of nonsynonymous mutations and still be functional.

Data and Files

Only sequences from visit 1 and visit 4 exist within each subject's sequence file.

Total Clones: 64



Matt Allegretti and I were in contact about our research presentation via Google Drive. He also helped orient me regarding the requirements of this weeks lab entry. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Other Links

User Page: Anindita Varshneya

Bioinfomatics Lab: Fall 2016

Class Page: BIOL 368-01: Bioinfomatics Laboratory, Fall 2016

Weekly Assignments Individual Journal Assignments Shared Journal Assignments

SURP 2015

Links: Electronic Lab Notebook