BIOL398-01/S10:Class Journal Week 9

Kristoffer Chin

BIOL398-01/S10:Week 9

Kristoffer Chin: Week 9

1. The purpose of this assignment was to independently study the HIV structure in a group. It was much like the HIV evolution project in which we were required to select HIV patient subjects, visits, and clones from the Markham study. It lets use utilize bioinformatics tools to analyze the structure of these sequences that were given to us in order to understand the structure of the HIV.
2. I learned how to better understand the ProtPram tool used for comparing amino acids and looking at the protein structures of amino acid sequence. I was also able to utilize past tools, such as the workbench which means that all of these tools are practiced on because they all work together
3. At the moment, I have no questions.

Salomon Garcia

1. The overall objective of this assignment was to make sure to work as a group to figure out and comprehend the structure of HIV. In order to do this task we would need to work with previous information from the Markham paper as well with the previous tools that we learned such as the case with Biology Workbench and at the same time we learned to use new tools that helped with the creation of 3D models of the proteins we gathered.
2. Some of things that I learned how to use quite well were how to use biology workbench and make a 3D model by making a boxshade once the sequence has been aligned and imported. One other thing that I learn to use but not quite as extensively was the ProtPram Tools.
3. At this time I have no questions.

Salomon Garcia Valencia 19:17, 21 March 2010 (EDT)

Ryan Willhite

1. What was the purpose of this assignment? The purpose of the assignment was to rephrase our previous question but using protein sequences instead of nucleic sequences to further investigate the questions we had on the markham paper. Using workbench, and the book "Bioinformatics for Dummies," we were able to utilize these skills to experiment and test in the area of biochemistry.
2. What did I learn from this assignment (head, hands, heart)? I learned so much from this task simply because I have never taken biochemistry before. It is a different world in my eyes and I am finding that nucleic sequences may not be the most efficient way of looking for clue but in the protein developed from these sequences. They function entirely different and this is apparent when looking at differences in results from the previous presentation with no to little answers, but some interesting findings to some sort of conclusion as to at least the best method of categorizing progression. Although, what we hoped to find was not found, I learned that these tools online are very informative and helpful in our research. I also feel a lot more comfortable using these programs.
3. What did I not understand (yet) about this assignment? I thought that one of the programs we have used was a bit confusing and still unsure how to use this ProScan tool on the expasy.org site.

Ryan N. Willhite 15:32, 21 March 2010 (EDT)

• Week 9 Assignment Page

• Week 9 Journal