Chris Rhodes Week 3: Difference between revisions
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==Methods== | ==Methods== | ||
'''Activity 1 Parts 2 and 3''' | '''Activity 1 Parts 2 and 3''' | ||
* | *Following the Genbank links from the [http://www.ncbi.nlm.nih.gov/pubmed?term=Patterns%20of%20HIV-1%20Evolution%20in%20individuals%20with%20differing%20rates%20of%20CD4|PubMed article] under Secondary Source ID I added the Fasta sequence of AF016760, AFO016761, AFO016767, AFO016780, and AFO016787 to the [http://workbench.sdsc.edu|WorkBench] nucleotide tools and ran a ClustalW multiple sequence allignment using the default parameters: | ||
[[Image:CHR_Image1_20110914.jpg|HIV-1 Nucleotide Sequence Alignment]] | [[Image:CHR_Image1_20110914.jpg|HIV-1 Nucleotide Sequence Alignment]] | ||
*I also looked at the unrooted genetic tree and took a screenshot: | *I also looked at the unrooted genetic tree and took a screenshot: | ||
Line 7: | Line 7: | ||
'''Activity 2 Part 1''' | '''Activity 2 Part 1''' | ||
*I added all of the nucleic acid sequences of both .txt files onto the | *I added all of the nucleic acid sequences of both .txt files onto the Workbench by uploading each .txt file into the nucleotide sequences section of Workbench. The .txt files can be found here [[BIOL368/F11:HIV_Evolution#In-class_Activity| HIV-1 In-Class Activity Page]] under the background section along with a link to the Activity handout and the general requirements of the assignment. | ||
*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: | *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.jpg|Selected ClustalW Alignment of Subjects 12, 13, 14 and 15]] | *[[Image:CHR_Image3_20110914.jpg|Selected ClustalW Alignment of Subjects 12, 13, 14 and 15]] |
Revision as of 20:49, 19 September 2011
Methods
Activity 1 Parts 2 and 3
- Following the Genbank links from the article under Secondary Source ID I added the Fasta sequence of AF016760, AFO016761, AFO016767, AFO016780, and AFO016787 to the [1] nucleotide tools and ran a ClustalW multiple sequence allignment using the default parameters:
- I also looked at the unrooted genetic tree and took a screenshot:
Activity 2 Part 1
- I added all of the nucleic acid sequences of both .txt files onto the Workbench by uploading each .txt file into the nucleotide sequences section of Workbench. The .txt files can be found here HIV-1 In-Class Activity Page under the background section along with a link to the Activity handout and the general requirements of the assignment.
- 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:
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.
- This was also done for Subject 9
- and Subject 10
- 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)
- Using Subjects 12 and 13 I created a new alignment to check the Min and Max differences across subjects by using Clustdist
- This was repeated using a Subject 8 and 9 alignment and a Subject 8 and 10 alignment.
- 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
- 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.
Markham Paper Prep
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