1. Using BLAST and ClustalW2 for Multiple Sequence Alignment IBGP/BMI705 Lab 2 January 14, 2009 Lee Cooper, TA IBGP705@gmail.com

2. Have you ever used bioinformatics tools?

3. Why should I care about understanding bioinformatics? Applicable Focus benchwork Preliminary data Free, readily-available tools vast amounts of information powerful Required knowledge in 5-10 years Career marketability

4. Summary: BLAST/ Sequence Alignment A—Search genes (5 minutes) B—BLAST (10 minutes) C—Pair BLAST (10 minutes) D—ClustalW2 (10 minutes)

5. Today’s guided lab: BLAST/ Sequence Alignment Follow handout Ask questions Work together Answer questions short-answer format on paper turn in to TA today (Pass/fail) Next week’s lab– SAME handout and tools Practice outside of class How can you use these tools to help along your current research and/or studies?

6. A. Search for gene/s

11. B. BLAST

14. C. Pair BLAST: Comparing Homo sapiens E2F3 to Mus musculus E2f3

16. D. ClustalW2 Sequence Alignment