Zachary T. Goldstein Week 4: Difference between revisions

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==Part II==
==Part II==
*Selected all the clones from subjects 3, 14, and 1 respectivelty and ran separate alignments on set of sequences from each subject be selecting them and pressing "CLUSTALW" and "run"
*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
* 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)
*Data was entered into Table 2 (below)
Line 43: Line 43:
**:Subject 1-  8.38
**:Subject 1-  8.38
*Min and Max differences were calculated via the Clustdist tool in the alignment tool set
*Min and Max differences were calculated via the Clustdist tool in the alignment tool set
*A distance matrix for each set of allignments (3) was completed and a table was produced
*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 multipled by 285 (representing the length of the sequence)
*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
*This was done to convert that percentage difference score into the raw number of differences
*Results were rounded to the nearest integer (Table 2)
*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-1 max-41
**1 vs 2: min- max-
**2 vs 3: min- max-


=Results=
=Results=

Revision as of 11:53, 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

Figure 1
  • 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
  • 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-1 max-41
    • 1 vs 2: min- max-
    • 2 vs 3: min- max-

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:


All individual assignments:


All shared journals:

User: Zachary T. Goldstein

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