Matthew K. Oki Individual Journal 9
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Week 9 Individual Journal
Purpose
Methods & Results
- Convert DNA Sequences to protein sequences in ExPASY Translate tool
- Below is an example of the output of the DNA to protein sequence conversion. They are separated into six reading frames.
- How do you know which of the six frames is the correct reading frame (without looking up the answer)?
- We knew the correct reading frame was the one that had a sequence with no stop codon in it.
- How do you know which of the six frames is the correct reading frame (without looking up the answer)?
- Find out what is already known about the HIV gp120 envelope protein in 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?
- There are 206,278 results
- Entry P04578 was looked up and observed. What types of information are provided about this protein?
- Function, taxonomy, location on the subcellular level, pathology, processing, interaction, family and domain, sequence, cross-references, and miscellaneous information are all provided on this protein page.
- PredictProtein server was used to analyze only the V3 region of the Markham et al. (1998) sequences.
- An amino acid sequence from Markham et al. (1998) was placed in the database and analyzed.
- How does this information relate to what is stored in the UniProt database?
- This was an interesting figure because it described possible binding sites, bond locations, and secondary structure locations. It also links back to the UniProt database for certain target alignments.
- If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
- Protein Structure from Kwong et al. (1998) was downloaded and opened in Cn3D software site. The picture of the result is posted below
- Find the N-terminus and C-terminus of each polypeptide tertiary structure.
- Each terminus of each polypeptide was found by looking for the ends of each polypeptide. By using the coloring shortcuts, this process of finding the ends was sped up.
- Locate all the secondary structure elements. Does this match the predictions made by the PredictProtein server?
- The PredictProtein server gave us a prediction of two helices and six beta sheets. This was seen exactly in the Cn3D program rendering of the Kwong et al. (1998) structure.
- Locate the V3 region and figure out the location of the Markham et al. (1998) sequences in the structure.
Data & Files
Scientific Conclusion
Defining Our Research Project
- Our Question:
- Our Prediction:
- Which subjects, visits, and clones will you use to answer your question?
Acknowledgments
References
Class Homework Links
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My Home Page: Matthew K. Oki
Class Home Page: Bioinformatics Home Page
My Paper Resume: Matthew K. Oki Resume