Salomon Garcia: Week 4

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Contents

Week 4 Entry

Activity 1 Part 1

  • Pubmed:
  1. How did you searh for the PubMed entry?
  2. What oher ways might you have searched?
  3. What other types of related information are available?
Pubmed search
Pubmed search
  1. I searched for the original paper by typing in the entire title of the research paper into the search box and the window showed the paper that was written in 1998.
  2. Another way I could have searched for it was by doing an advanced search and using the authors name on the search.
  3. There were other information that was useful as was the information that described what HIV-1 is.

Activity 1 Part 2

  • GenBank:
  1. What was the accession number of the sequence you chose?
  2. Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from?
  1. The accession number was GenBank: AF016760.1.
  2. This sequence was from subject 1. GenBank and the Fasta both contain where the section of HIV came from.

Activity 1 Part 3

  • In this portion of the activity I used 4 of the sequences from the Markham study. I ran a ClustalW with the Biology workbench website. this was the sequence:
Sequences
Sequences
  • This is a pic of the experimental tree:
Experimental Tree
Experimental Tree


Activity 2 Part 1

  • Sequences were generated and this is what is seen:
Sequences
Sequences
  • A rooted tree was also generated and this is what was shown:
Rooted Tree
Rooted Tree

BIOL 398-01: Bioinformatics Lab

  • Lab Journal
Salomon Garcia: Week 2 Salomon Garcia: Week 6 Salomon Garcia: Week 11
Salomon Garcia: Week 3 Salomon Garcia: Week 7 Salomon Garcia: Week 12
Salomon Garcia: Week 4 Salomon Garcia: Week 8 Salomon Garcia: Week 13
Salomon Garcia: Week 5 Salomon Garcia: Week 9 Salomon Garcia: Week 14


  • Shared Journal
  1. BIOL398-01/S10:Class Journal Week 2
  2. BIOL398-01/S10:Class Journal Week 3
  3. BIOL398-01/S10:Class Journal Week 4
  4. BIOL398-01/S10:Class Journal Week 5
  5. BIOL398-01/S10:Class Journal Week 6
  6. BIOL398-01/S10:Class Journal Week 7
  7. BIOL398-01/S10:Class Journal Week 8
  8. BIOL398-01/S10:Class Journal Week 9
  9. BIOL398-01/S10:Class Journal Week 11
  10. BIOL398-01/S10:Class Journal Week 12
  11. BIOL398-01/S10:Class Journal Week 13
  12. BIOL398-01/S10:Class Journal Week 14


  • Assignments
  1. BIOL398-01/S10:Week 2
  2. BIOL398-01/S10:Week 3
  3. BIOL398-01/S10:Week 4
  4. BIOL398-01/S10:Week 5
  5. BIOL398-01/S10:Week 6
  6. BIOL398-01/S10:Week 7
  7. BIOL398-01/S10:Week 8
  8. BIOL398-01/S10:Week 9
  9. BIOL398-01/S10:Week 11
  10. BIOL398-01/S10:Week 12
  11. BIOL398-01/S10:Week 13
  12. BIOL398-01/S10:Week 14

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