Zachary T. Goldstein Week 4: Difference between revisions
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Revision as of 16:12, 21 September 2016
Purpose
Methods
Part I
- Uploaded the “visit_1_S1_S9.txt” and “visit_1_S10_S15.txt” files into the nucleic
acid tool set of the Biology Workbench by saving to ThawSpace
- Two data files were used because the Biology Workbench only allows up to 64
sequences to be uploaded at a time
- Generated a multiple sequence alignment and distance tree for 12 of these sequences (below)
- S15V1-7
- S15V1-8
- S15V1-9
- S10V1-6
- S10V1-5
- S10V1-4
- S1V1-2
- S1V1-3
- S1V1-4
- S6V1-1
- S6V1-2
- S6V1-3
- Unrooted tree was created using Biology Workbench
- Selected sequences
- Selected "CLUSTALW" and then "Submit"
- The clones from each subject clustered together (Figure 1) however subject 15's sequences were more spread out than others
- Some subjects’ clones show more diversity than others. This is observable by tracing the length of lines connecting the sequences from the same subject (ex: S15 and S1) (Figure 1)
- None of the subjects really clustered together however it is difficult to differentiate the lengths of the terminal branches due to the lack of a definitive evolutionary beginning
- Observations of the tree:
- There is a clear close relationship between the sequences from the same subjects
- Sequences from subject 10 and 6 appear on opposite sides of the tree indicating a possible distant relationship
- There are otherwise no clear relationships between subjects' sequences due to no clear pattern of closeness of nodes
- The Unrooted Tree was saved and uploaded to this assignment (right)
Part II
- Selected all the clones from subjects 3, 14, and 1 respectively and ran separate alignments on set of sequences from each subject be selecting them and pressing "CLUSTALW" and "run"
- From the alignment 'S' values were calculated by counting the number of positions where there was at least one nucleotide difference across the collection of clones indicated by text not illuminated in blue
- Data was entered into Table 2 (below)
- Theta (θ) was calculated using formula provided in assignment and values were included in Table 2
- Theta calculations:
- Subject 3- 3.27
- Subject 14- 2.63
- Subject 1- 8.38
- Theta calculations:
- Min and Max differences were calculated via the Clustdist tool in the alignment tool set
- A distance matrix for each set of alignments (3) was completed and a table was produced
- The smallest and largest numbers were identified in the table and each were separately multiplied by 285 (representing the length of the sequence)
- This was done to convert that percentage difference score into the raw number of differences
- Results were rounded to the nearest integer (Table 2)
- Total sequences were compared to each other by importing sequences from 2 subjects and using the same procedure above (Table 3)
- 1 vs 3: min-0 max-41
- 1 vs 14: min-0 max-26
- 3 vs 14: min-1 max-42
Subject | Number of Clones | "S" Value | Theta (θ) | Min Difference | Max Difference | |
---|---|---|---|---|---|---|
row 1, cell 1 | row 1, cell 2 | row 1, cell 3 | ||||
row 2, cell 1 | row 2, cell 2 | row 2, cell 3 |
Results
Conclusion
Acknowledgments
- I received help on this assignment from User:Shivum A Desai
- While I received help on this page everything completed for this assignment was done by me and was not copied from anyone else
References
Category: BIOL368/F16:People BIOL368/F16
All class assignments:
- Week 1 Assignment
- Week 2 Assignment
- Week 3 Assignment
- Week 4 Assignment
- Week 5 Assignment
- Week 6 Assignment
- Week 7 Assignment
- Week 8 Assignment
- Week 9 Assignment
- Week 10 Assignment
- Week 11 Assignment
- Week 14 Assignment
- Week 15 Assignment
All individual assignments:
- Zachary T. Goldstein Week 2
- Zachary T. Goldstein Week 3
- Zachary T. Goldstein Week 4
- Zachary T. Goldstein Week 5
- Zachary T. Goldstein Week 6
- Zachary T. Goldstein Week 7
- Zachary T. Goldstein Week 8
- Zachary T. Goldstein Week 9
- Zachary T. Goldstein Week 10
- Zachary T. Goldstein Week 11
- Zachary T. Goldstein Week 14
- Zachary T. Goldstein Week 15
All shared journals:
- BIOL368/F16:Class Journal Week 1
- BIOL368/F16:Class Journal Week 2
- BIOL368/F16:Class Journal Week 3
- BIOL368/F16:Class Journal Week 4
- BIOL368/F16:Class Journal Week 5
- BIOL368/F16:Class Journal Week 6
- BIOL368/F16:Class Journal Week 7
- BIOL368/F16:Class Journal Week 8
- BIOL368/F16:Class Journal Week 9
- BIOL368/F16:Class Journal Week 10
- BIOL368/F16:Class Journal Week 11
- BIOL368/F16:Class Journal Week 14
- BIOL368/F16:Class Journal Week 15