Mia Huddleston Week 9: Difference between revisions
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*We decided, for simplicity, to only look at nonprogressor and rapid progressors to have a clear difference if possible. | *We decided, for simplicity, to only look at nonprogressor and rapid progressors to have a clear difference if possible. | ||
*We also decided to only look at the first to last visit of each of the subjects we choose from both of the progressor groups. | *We also decided to only look at the first to last visit of each of the subjects we choose from both of the progressor groups. | ||
*We then chose two subjects in each the nonprogressors and rapid progressors | |||
**Subjects 3 and 10 | |||
*Then, we converted our DNA sequences into protein sequences using the ExPASY Translate tool | |||
**How do you know which of the six frames is the correct reading frame (without looking up the answer)? | |||
***We know which of the reading frames is correct by which ones do not have stop condons in the middle of the reading frame since this sequence was taken from the middle of a complete open reading frame as seen in the picture below | |||
[[Media:Screen Shot 2016-10-25 MH.png]] | |||
*We then can find the rest of our sequence data from from the BEDROCK HIV Problem Space. | |||
*To learn more about HIV gp120 envelope, we explored the UniProt Knowledgebase (UniProt KB) | |||
**If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get? | |||
***206,278 results | |||
**What types of information are provided about this protein in this database entry? | |||
***This database gives information on the function, molecular function, and the biological process of this protein. | |||
*We then used the PredictProtein server and imputed one of our amino acid sequences (S3V1-1) into the input field to predict the protein. A picture of the results can be seen below. | |||
[[Media:ProteinS3V1-1MH.png]] | |||
**How does this information relate to what is stored in the UniProt database? | |||
***This gives you a lot of specific information about this sequence and the possible function just as UniProt did. | |||
#What is your question? | #What is your question? | ||
Revision as of 16:44, 25 October 2016
Electronic Notebook
Purpose
The purpose of this lab is to choose a topic for my HIV structure research project and begin research on the project.
Methods and Results
- When developing a question to research, Avery and I decided to look into how sequence changes of amino acids may be different for each progressor group.
- We decided, for simplicity, to only look at nonprogressor and rapid progressors to have a clear difference if possible.
- We also decided to only look at the first to last visit of each of the subjects we choose from both of the progressor groups.
- We then chose two subjects in each the nonprogressors and rapid progressors
- Subjects 3 and 10
- Then, we converted our DNA sequences into protein sequences using the ExPASY Translate tool
- How do you know which of the six frames is the correct reading frame (without looking up the answer)?
- We know which of the reading frames is correct by which ones do not have stop condons in the middle of the reading frame since this sequence was taken from the middle of a complete open reading frame as seen in the picture below
- How do you know which of the six frames is the correct reading frame (without looking up the answer)?
Media:Screen Shot 2016-10-25 MH.png
- We then can find the rest of our sequence data from from the BEDROCK HIV Problem Space.
- To learn more about HIV gp120 envelope, we explored the UniProt Knowledgebase (UniProt KB)
- If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
- 206,278 results
- What types of information are provided about this protein in this database entry?
- This database gives information on the function, molecular function, and the biological process of this protein.
- If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
- We then used the PredictProtein server and imputed one of our amino acid sequences (S3V1-1) into the input field to predict the protein. A picture of the results can be seen below.
- How does this information relate to what is stored in the UniProt database?
- This gives you a lot of specific information about this sequence and the possible function just as UniProt did.
- How does this information relate to what is stored in the UniProt database?
- 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?
- You should choose a combination of subjects, visits, and clones that will add up to approximately 50 sequences. You will need about that many sequences to answer a reasonably complex question. However, you cannot use more because the multiple sequence alignment tool cannot handle more than that many sequences.
- Justify why you chose the subjects, visits, and clones you did.
Conclusion
Data and Files
Acknowledgements
References
Useful links
User Page: Mia Huddleston
Bioinfomatics Lab: Fall 2016
Class Page: Bioinfomatics Laboratory, Fall 2016
