Chris Rhodes Week 3

Methods

Activity 1 Part 2 and 3

1. From GenBank I added the Fasta sequence of AF016760, AFO016761, AFO016767, AFO016780, and AFO016787 to the WorkBench nucleotide tools, ran a ClustalW multiple sequence allignment using the default parameters and took a screenshot:File:CHR Image1 20110914
2. I also looked at the unrooted genetic tree and took a screenshot: File:CHR Image2 20110914

Activity 2 Part 1

1. I added the nucleic acid sequence of both .txt files on the WorkBench.
2. From the sequences I ran a ClustalW allignment of: S12V1-1, S12V1-2, S12V1-3, S13V1-2, S13V1-3, S13V1-4, S14V1-4, S14V1-5, S14V1-6, S15V1-10, S15V1-11, S15V1-12 and took a screenshot of the alignment and the unrooted genetic tree: File:CHR Image3 20110914 File:CHR Image4 20110914

Activity 2 Part 2

1. To calculate the S value of a particular alignment I selected all of Subject 8's clones and ran a ClustalW alignment.Subject 8 Alignment

This was also done for Subject 9 Subject 9 Alignment and Subject 10 Subject 10 Alignment

1. From these alignments S and Theta were calculated and using Clustdist for each alignment the Min and Max differences were determined. (See Results: Activity 2 Part 2: Analysis Table)Clustdist Subject 8Clustdist Subject 9Clustdist Subject 10
2. Using Subjects 12 and 13 I created a new alignment to check the Min and Max differences across subjects by using Clustdist Subject 12 and 13 AlignmentClustdist Subjects 12 and 13
3. This was repeated using a Subject 8 and 9 alignment and a Subject 8 and 10 alignment. Clustdist Subjects 8 and 9Clustdist Subjects 8 and 10
4. Using the Clustdist of all the subject cross alignments the Min and Max differences for each were calculated. (See Results: Activity 2, Part 2: Cross Subject Alignment Table)

Results

Activity 2, Part 2: Single Subject Alignment Table

Subject  Clones  S  Theta  Min-Diff.  Max-Diff.
8        5       6  2.88   1.14       5.13
9        5       5  2.44   1.99       3.99
10       7       7  2.86   1.14       3.14

Activity 2, Part 2: Cross Subject Alignment Table

Subject Crosses  Min-Diff.  Max-Diff.
12 and 13        39.05      43.89
8 and 9          27.93      33.06
8 and 10         27.1       31.07

Questions

Activity 1, Part 2: GenBank

1. AF016760, AFO016761, AFO016767, AFO016780, and AFO016787
2. These gene sequences all came from subject 1

Activity 2, Part 1

1. Clones from each subject tend to cluster together on the unrooted genetic tree
2. Some subject clusters are much closer to each other on the tree than others specifically Subjects 13,14,and 15
3. From the pattern of clustering seen in the genetic tree it seems that the genetic tree separates individual sequences based on their similarity to each other. The closer one sequence is to another on the tree, the more closely those two sequences are related to each other in terms of sequence similarity or evolutionary time.

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