1. Wednesday, September 11, 2013 TAKE OUT: Bioinformatics pre-lab (p. 1-2); tear off pages 3-8 from lab handout AND RECYCLE ! SAVE analysis questions on page 9 PROCESS-BASED TARGET: D.Evaluate BLAST sequences to determine evolutionary relationships between organisms HOMEWORK: Complete bioinformatics lab PARTS A and B Print screen shots & completed cladograms as described in lab procedure Answer analysis Q’s on last page of handout (on separate paper) – ALL ITEMS DUE Monday, Sept. 16 TAKE OUT: Bioinformatics pre-lab (p. 1-2); tear off pages 3-8 from lab handout AND RECYCLE ! SAVE analysis questions on page 9 PROCESS-BASED TARGET: D.Evaluate BLAST sequences to determine evolutionary relationships between organisms HOMEWORK: Complete bioinformatics lab PARTS A and B Print screen shots & completed cladograms as described in lab procedure Answer analysis Q’s on last page of handout (on separate paper) – ALL ITEMS DUE Monday, Sept. 16

2. Pre-Lab Warm Up Share and discuss your answer to the pre-lab question item # indicated on the sticky note at your table with your shoulder partner Generate a thorough answer after discussion and write your answer on the white board

3. Bioinformatics Pre-Lab Questions 1.Define bioinformatics 2.Name the protein studied in the lab. 3.Name ONE online tool you’ll use to to analyze amino acid sequences across species. 4.What is an outgroup? What is the name of the outgroup organism for Part A? 5.What is a phylogenetic tree (cladogram)? Do the lengths of the branches indicate evolutionary time? Explain. 6.Identify one marine mammal & one terrestrial (land) animal compared in Part B.

4. Bioinformatics Pre-Lab Question #7 Obtain HBB amino acid sequence (FASTA file) for variety of marine & terrestrial mammals Align amino acid sequences Quantify similarities & differences between amino acid sequences using online tool Use quantitative data to construct cladogram inferring evolutionary relationships between species Evaluate if hypothesis is supported or refuted using cladogram Generate hypothesis about suspected evolutionary relationships between marine & terrestrial species

5. Part A & B Questions & Hypothesis Will HBB amino acid sequence comparison determine that all marine mammals are closely related to each other and descended from one, recent common ancestor? If marine mammals are more closely related to each other, then whales & seals will share a recent common ancestor that is different from dogs and cows.

6. Bioinformatics Lab Changes We’ll use GenBank instead of NGBW to locate the amino acid sequence of the hemoglobin protein for a variety of species Amino acid sequences will be aligned and analyzed by Clustal Omega Phylogenetic trees will be created using Clustal W2_phylogeny OR http://www.genome.jp/tools/clustalw if you are having “JAVA” issues on computer http://www.genome.jp/tools/clustalw

7. Bioinformatics Lab Changes 16. Open another tab in web browser 17. Go to website: http://www.genome.jp/tools/clustalwhttp://www.genome.jp/tools/ 18. Copy & paste amino acid sequences (FASTA format) into box at top of page with organisms’ names 19. Scroll down and click “Execute Multiple Alignment” 20. Scroll down and from drop down menu, highlight “Rooted phylogenetic tree (UPGMA)” and click “EXEC” button 21. Take a screen shot of cladogram and paste screen shot into Word document with color aligned sequence

8. 18. 19. 20.

9. Bioinformatics Lab Changes Protein is at the TOP of the list in pull down menu! It’s not at the bottom with the “P”’s

10. Bioinformatics Lab is the SAME… Following directions is VERY important; read & think BEFORE completing steps! Make a document with FASTA amino acid sequences. File names are important. Save document as.txt. Take a screen shot of amino acid sequence alignments (page 6, step #15) for Parts A & B and paste into a word document Take a screen shot of completed cladogram (page 6, step #20) for Parts A & B & paste into a word document