Chris Rhodes Week 3: Difference between revisions
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==Methods== | ==Methods== | ||
'''Activity 1 Part 2 and 3''' | |||
#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:[[Image:CHR_Image1_20110914]] | #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:[[Image:CHR_Image1_20110914]] | ||
#I also looked at the unrooted genetic tree and took a screenshot: [[Image:CHR_Image2_20110914]] | #I also looked at the unrooted genetic tree and took a screenshot: [[Image:CHR_Image2_20110914]] | ||
'''Activity 2 Part 1''' | |||
#I added the nucleic acid sequence of both .txt files on the WorkBench. | #I added the nucleic acid sequence of both .txt files on the WorkBench. | ||
#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: [[Image:CHR_Image3_20110914]] [[Image:CHR_Image4_20110914]] | #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: [[Image:CHR_Image3_20110914]] [[Image:CHR_Image4_20110914]] | ||
'''Activity 2 Part 2''' | |||
#To calculate the S value of a particular alignment I selected all of Subject 8's clones and ran a ClustalW alignment.[[Image:CHR_Image5_20110914]] | #To calculate the S value of a particular alignment I selected all of Subject 8's clones and ran a ClustalW alignment.[[Image:CHR_Image5_20110914]] | ||
This was also done for Subject 9 [[Image:CHR_Image6_20110914]] | This was also done for Subject 9 [[Image:CHR_Image6_20110914]] | ||
and Subject 10 [[Image:CHR_Image7_20110914]] | and Subject 10 [[Image:CHR_Image7_20110914]] | ||
#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)[[Image:CHR_Image8_20110914]] | #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)[[Image:CHR_Image8_20110914]][[Image:CHR_Image9_20110914]][[Image:CHR_Image10_20110914]] | ||
#Using Subjects 12 and 13 I created a new alignment | |||
==Results== | ==Results== | ||
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#Clones from each subject tend to cluster together on the unrooted genetic tree | #Clones from each subject tend to cluster together on the unrooted genetic tree | ||
#Some subject clusters are much closer to each other on the tree than others specifically Subjects 13,14,and 15 | #Some subject clusters are much closer to each other on the tree than others specifically Subjects 13,14,and 15 | ||
#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. | |||
{{Chris H. Rhodes}} | {{Chris H. Rhodes}} |
Revision as of 15:44, 14 September 2011
Methods
Activity 1 Part 2 and 3
- 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
- I also looked at the unrooted genetic tree and took a screenshot: File:CHR Image2 20110914
Activity 2 Part 1
- I added the nucleic acid sequence of both .txt files on the WorkBench.
- 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
- To calculate the S value of a particular alignment I selected all of Subject 8's clones and ran a ClustalW alignment.File:CHR Image5 20110914
This was also done for Subject 9 File:CHR Image6 20110914 and Subject 10 File:CHR Image7 20110914
- 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)File:CHR Image8 20110914File:CHR Image9 20110914File:CHR Image10 20110914
- Using Subjects 12 and 13 I created a new alignment
Results
Activity 2, Part 2: Analysis 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
Questions
Activity 1, Part 2: GenBank
- AF016760, AFO016761, AFO016767, AFO016780, and AFO016787
- These gene sequences all came from subject 1
Activity 2, Part 1
- Clones from each subject tend to cluster together on the unrooted genetic tree
- Some subject clusters are much closer to each other on the tree than others specifically Subjects 13,14,and 15
- 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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