Salomon Garcia: Week 4
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Week 4 Entry
Activity 1 Part 1
- Pubmed:
- How did you searh for the PubMed entry?
- What oher ways might you have searched?
- What other types of related information are available?
![](https://s3-us-west-2.amazonaws.com/oww-files-thumb/1/1c/Search_1.jpg/550px-Search_1.jpg)
- 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.
- Another way I could have searched for it was by doing an advanced search and using the authors name on the search.
- There were other information that was useful as was the information that described what HIV-1 is.
Activity 1 Part 2
- GenBank:
- What was the accession number of the sequence you chose?
- Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from?
![](https://s3-us-west-2.amazonaws.com/oww-files-thumb/4/49/Picture_3.jpg/550px-Picture_3.jpg)
- The accession number was GenBank: AF016760.1.
- 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:
![](https://s3-us-west-2.amazonaws.com/oww-files-thumb/7/7e/Sequence_alignment.jpg/500px-Sequence_alignment.jpg)
- This is a pic of the experimental tree:
![](https://s3-us-west-2.amazonaws.com/oww-files-thumb/2/2d/Tree.jpg/500px-Tree.jpg)
Activity 2 Part 1
- Sequences were generated and this is what is seen:
- A rooted tree was also generated and this is what was shown:
BIOL 398-01: Bioinformatics Lab
- Lab Journal
- Shared Journal
- BIOL398-01/S10:Class Journal Week 2
- BIOL398-01/S10:Class Journal Week 3
- BIOL398-01/S10:Class Journal Week 4
- BIOL398-01/S10:Class Journal Week 5
- BIOL398-01/S10:Class Journal Week 6
- BIOL398-01/S10:Class Journal Week 7
- BIOL398-01/S10:Class Journal Week 8
- BIOL398-01/S10:Class Journal Week 9
- BIOL398-01/S10:Class Journal Week 11
- BIOL398-01/S10:Class Journal Week 12
- BIOL398-01/S10:Class Journal Week 13
- BIOL398-01/S10:Class Journal Week 14
- Assignments
- BIOL398-01/S10:Week 2
- BIOL398-01/S10:Week 3
- BIOL398-01/S10:Week 4
- BIOL398-01/S10:Week 5
- BIOL398-01/S10:Week 6
- BIOL398-01/S10:Week 7
- BIOL398-01/S10:Week 8
- BIOL398-01/S10:Week 9
- BIOL398-01/S10:Week 11
- BIOL398-01/S10:Week 12
- BIOL398-01/S10:Week 13
- BIOL398-01/S10:Week 14