Matthew K. Oki Individual Journal 4: Difference between revisions
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#Three individual subjects were run through multiple sequence alignment | #Three individual subjects were run through multiple sequence alignment | ||
#*Each nucleotide difference (S) was denoted by the absence of a star as shown below with Subject 15: | #*Each nucleotide difference (S) was denoted by the absence of a star as shown below with Subject 15: | ||
[[Image:mattokiScreen_Shot_2016-09-20_at_4.03.35_PM.png]] | [[Image:mattokiScreen_Shot_2016-09-20_at_4.03.35_PM.png|600x600px]] | ||
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#Theta was then calculated: | #Theta was then calculated: | ||
#*Theta is an estimate of the average pairwise genetic distance | #*Theta is an estimate of the average pairwise genetic distance | ||
#*The equation from [[Media:Exploring_HIV_Evolutionmattoki.pdf| Exploring HIV Evolution]] is given below: | #*The equation from [[Media:Exploring_HIV_Evolutionmattoki.pdf| Exploring HIV Evolution]] is given below: | ||
[[Image:mattokiScreen_Shot_2016-09-21_at_3.23.25_PM.png]] | [[Image:mattokiScreen_Shot_2016-09-21_at_3.23.25_PM.png|mattokiScreen_Shot_2016-09-21_at_3.23.25_PM.png]] | ||
#Min and Max difference were calculated: | #Min and Max difference were calculated: | ||
#*One subject's clones were selected and run through the same multiple sequence alignment | #*One subject's clones were selected and run through the same multiple sequence alignment | ||
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#*Run a "Clustaldist" test | #*Run a "Clustaldist" test | ||
#*A matrix is produced as shown below: | #*A matrix is produced as shown below: | ||
[[Image:mattokiScreen_Shot_2016-09-21_at_3.32.49_PM.png]] | [[Image:mattokiScreen_Shot_2016-09-21_at_3.32.49_PM.png|500x300px]] | ||
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*The highest and lower numbers in this matrix were multiplied by the length of sequence | *The highest and lower numbers in this matrix were multiplied by the length of sequence | ||
**Rounding these numbers to the nearest integer gives us maximum and minimum respectively | **Rounding these numbers to the nearest integer gives us maximum and minimum respectively | ||
*This was performed for all 3 of the subjects picked above with the results in the table below: | *This was performed for all 3 of the subjects picked above with the results in the table below: | ||
[[Image:graph2mattokiScreen_Shot_2016-09-24_at_7.43.12_PM.png]] | [[Image:graph2mattokiScreen_Shot_2016-09-24_at_7.43.12_PM.png|400x300px]] | ||
*Finally, the min and max were calculated from a comparison of two subjects: | *Finally, the min and max were calculated from a comparison of two subjects: | ||
**The table below gives the results of three comparisons: | **The table below gives the results of three comparisons: | ||
[[Image:graph3mattokiScreen_Shot_2016-09-24_at_7.43.22_PM.png]] | [[Image:graph3mattokiScreen_Shot_2016-09-24_at_7.43.22_PM.png|400x300px]] | ||
==Scientific Conclusion== | ==Scientific Conclusion== |
Revision as of 20:00, 24 September 2016
Matthew K. Oki I.J. Week 4
Purpose
Methods & Results
- The formal methods were followed from Activity 2 of the Exploring HIV Evolution
Activity 2, Part 1
- Download the provided sequences of subjects 10-15 from BIOL368/F16:Week 4
- Upload these sequences into the Biology Workbench
- Run the multiple sequence alignment for the selected subjects and clones
- The subjects & clones below were used:
- The output results in the following uprooted tree:
Activity 2, Part 2
- Three individual subjects were run through multiple sequence alignment
- Each nucleotide difference (S) was denoted by the absence of a star as shown below with Subject 15:
- Theta was then calculated:
- Theta is an estimate of the average pairwise genetic distance
- The equation from Exploring HIV Evolution is given below:
- Min and Max difference were calculated:
- One subject's clones were selected and run through the same multiple sequence alignment
- Click on "Import Alignments"
- Go to the "Alignment Tool" tab
- Run a "Clustaldist" test
- A matrix is produced as shown below:
- The highest and lower numbers in this matrix were multiplied by the length of sequence
- Rounding these numbers to the nearest integer gives us maximum and minimum respectively
- This was performed for all 3 of the subjects picked above with the results in the table below:
- Finally, the min and max were calculated from a comparison of two subjects:
- The table below gives the results of three comparisons:
Scientific Conclusion
Defining Research Project
Question
Is there a genetic difference in HIV-1 in patients who contracted the virus sexually or by intravenous injection?
Hypothesis
We hypothesize that there will not be a genetic difference in HIV-1 in patients who contracted the virus sexually or by intravenous injection
Subjects, Visits, Clones
Class Homework Links
Weekly Assignments
Individual Journals
Class Journals
Other Links
My Home Page: Matthew K. Oki
Class Home Page: Bioinformatics Home Page
My Paper Resume: Matthew K. Oki Resume