Chris Rhodes Week 3: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(Formatting)
No edit summary
Line 3: Line 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: (Note: All ClustalW and Clusdist alignments were performed using the default parameters)
*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: (Note: All ClustalW and Clusdist alignments were performed using the default parameters)
[[Image:CHR_Image1_20110914.jpg|HIV-1 Nucleotide Sequence Alignment]]
[[Image:CHR_Image1_20110914.jpg|HIV-1 Nucleotide Sequence Alignment]]
The blue regions of the alignment represent where the nucleotides of the different sequences all match each other while the gray regions represent an area where at one nucleotide of at least one sequence differed from the nucleotides of the other sequences in the 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:  
[[Image:CHR_Image2_20110914.jpg|HIV-1 Alignment Unrooted Genetic tree]]
[[Image:CHR_Image2_20110914.jpg|HIV-1 Alignment Unrooted Genetic tree]]
The genetic tree shows the relative difference between all the sequences in the alignment. The closer the sequences are to each other the more similar the sequences are to each other.


'''Activity 2 Part 1'''
'''Activity 2 Part 1'''
Line 13: Line 15:


'''Activity 2 Part 2'''
'''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.
*To calculate the S value of a particular alignment I selected all of Subject 8's clones and ran a ClustalW alignment. The S value corresponds to the number of nucleotide sites of differing between any of the sequences aligned. For our purposes the S value can be found by counting the number of gray columns throughout the alignment. 
[[Image:CHR_Image5_20110914.jpg|Subject 8 Alignment]]
[[Image:CHR_Image5_20110914.jpg|Subject 8 Alignment]]
*This was also done for Subject 9
*This was also done for Subject 9

Revision as of 21:18, 19 September 2011

Methods

Activity 1 Parts 2 and 3

  • Following the Genbank links from the PubMed article under Secondary Source ID I added the Fasta sequence of AF016760, AFO016761, AFO016767, AFO016780, and AFO016787 to the WorkBench nucleotide tools and ran a ClustalW multiple sequence allignment using the default parameters: (Note: All ClustalW and Clusdist alignments were performed using the default parameters)

HIV-1 Nucleotide Sequence Alignment The blue regions of the alignment represent where the nucleotides of the different sequences all match each other while the gray regions represent an area where at one nucleotide of at least one sequence differed from the nucleotides of the other sequences in the alignment.

  • I also looked at the unrooted genetic tree and took a screenshot:

HIV-1 Alignment Unrooted Genetic tree The genetic tree shows the relative difference between all the sequences in the alignment. The closer the sequences are to each other the more similar the sequences are to each other.

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:
  • Selected ClustalW Alignment of Subjects 12, 13, 14 and 15
  • Unrooted Genetic Tree of Selected Sequences of Subjects 12, 13, 14, and 15

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. The S value corresponds to the number of nucleotide sites of differing between any of the sequences aligned. For our purposes the S value can be found by counting the number of gray columns throughout the alignment.

Subject 8 Alignment

  • This was also done for Subject 9

Subject 9 Alignment

  • and Subject 10

Subject 10 Alignment

  • From these alignments and using the equations given in the Activity Handout S and Theta were calculated.
  • By using the equations given in the Activity Handout and the Clustdist tool under the Alignment Tools section for each alignment the Min and Max differences were determined. (See Single Subject Alignment Table below)
  • Clustdist of Subject 8Clustdist Subject 8
  • Clustdist of Subject 9Clustdist Subject 9
  • Clustdist of Subject 10Clustdist Subject 10

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
  • 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 AlignmentSubject 12 and 13 Alignment
  • Subject 12 and 13 ClusdistClustdist Subjects 12 and 13
  • This was repeated using a Subject 8 and 9 alignment and a Subject 8 and 10 alignment.
  • Subject 8 and 9 ClustdistClustdist Subjects 8 and 9
  • Subject 8 and 10 ClustdistClustdist Subjects 8 and 10
  • Using the Clustdist of all the cross subject alignments the Min and Max differences for each were calculated. (Below)

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.

Markham Paper Prep

  • Vocab List
    1. Seroconverting:
    2. Sanger chain termination:
  1. Chris Rhodes User Page
  2. Week 2 Journal
  3. Week 3 Journal
  4. Week 4 Journal
  5. Week 5 Journal
  6. Week 6 Journal
  7. Week 7 Journal
  8. Week 8 Journal
  9. Week 9 Journal
  10. Week 10 Journal
  11. Week 11 Journal
  12. Week 12 Journal
  13. Week 13 Journal
  14. Week 14 Journal
  15. Home Page
  16. Week 5 Assignment Page
  17. Week 6 Assignment Page
  18. Week 7 Assignment Page
  19. Week 8 Assignment Page
  20. Week 9 Assignment Page
  21. Week 10 Assignment Page
  22. Week 11 Assignment Page
  23. Week 12 Assignment Page
  24. Week 13 Assignment Page
  25. Week 14 Assignment Page
Retrieved from "https://openwetware.org/mediawiki/index.php?title=Chris_Rhodes_Week_3&oldid=538858"