Bobak Seddighzadeh Week 4

Activity 1

Part 2: GenBank

• I downloaded four sequences in FASTA format to my local hard drive by selecting several at the same time in summary view.
• The accession number of the sequence I chose was: AF089154
• Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from? The HIV sequence was collected from subject 4. The sequence has a code that contains information about who the HIV was collected from. The code for this subject's particular sequence is S4V2-4 which indicates the clone is from subject four on his second visit, and its his fourth clone.
• These are the sequences I chose: HIV Sequences

Part 3: Introduction to the Biology Workbench

• To analyze the sequences I used Biology Workbench

1. Log onto Biology Workbench
2. Use nucleic sequence data
3. Select Add new sequences, press run; then upload your sequences
4. Select all your sequences and run a mucltiple sequence alignment using ClustalW

Activity 2

In this activity, I will use data sequences from fifteen individuals that participated in a study in Baltimore. I will proceed to characterize the poopulations of HIV within an individual and quantify the differences between the individuals. I will use ClustalW tool to build my alignments and distance based unrooted trees.

Part 1:

• Access sequencing information from Bedrock link on HIV assignment.
• Upload visit one from subjects 1 through 15 into the nucleic acid tool set of Biology Workbench.
• Preliminary analysis generate multiple sequence alignment and distance tree for 12 of these sequences
• Record the data of your clones in Table 2
• The following sequences were analyzed using ClustalW: Subject 1 clones 1,2,3; Subject 8 clones 1,2,3; Subject 5 clones 1,2,3; Subject 15 clones 1, 2, 3.

File:Activity2.png