BIOL368/F14:Chloe Jones Week 4
Exploring HIV Evolution In-Class Activity
Methods
Activity 1/Part 2: GenBank
Using the Genbank database, sequences were obtained from one of the fifteen subjects from the previously studied Markham et al. (1998) HIV-1 article .The sequence was chosen from a particular subject at a recorded visit, with a code for example that would read S4V2-4, signaling subject 4, visit 2. After a subject was selected the Genbank database allowed the viewing of the full record and the FASTA formatted sequence, which would be saved to a word document for further analysis in the proceeding activities.
Questions
- What was the accession number of the sequence you chose?
- ACCESSION: AF089142
- Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from?
- From subject 3, in the definition portion
Activity 1 // Part 3: Introduction to Biology Workbench
Based on random selection of 5 subjects sequence information obtained from activity 1/part 2, the FASTA formatted sequence would be be analyzed using the ClustalW tool which runs a multiple sequence alignment. The output is an unrooted tree the allows for pairwise similarity scores to be observed.
Activity 2 // Part 1: Quantifying Diversity Within and Between Subjects
Files labeled “Visit_1_Subjects_1_thru_9_HIV.txt” and “Visit_1_Subjects_10_thru_15_HIV.txt” were downloaded and uploaded into Biology Workbench. The files contained 97 sequences, and the program only allows 64, so they had to be uploaded separately. Multiple sequence alignment and the tree distance relationships were analyzed using the ClustalW tool, based on 12 sequences (3 clones from each of the 4 subjects), Unrooted tree of HIV-1 viral strains for subjects 15,14,13 and 12 for visit 1
