Homework #4 (130 points)

Assigned: 2/14/08 ---> Due: 2/26/08

There are three parts to this Gene Inspector homework. The trypsin sequences are contained in this Gene Inspector file. This is a file that you can "unstuff" with Stuffit Expander (Mac or Windows). If you cannot access the GI sequence file for some reason, the actual sequences themselves are available here as plain text - the trypsins are listed at the end of the protein sequences.

Part 1: Pairwise Alignment 40 points

Align the salmon and mosquito trypsin sequences using different standard tables and different gap penalties to determine what you consider to be the best alignment. Show several alignments and explain why your final one looks the best to you. These alignments should be an a GI notebook called GI_HW4.nbk.

Part 2: Scoring Table 50 points

Make up a scoring table of your own to align the same two sequences you aligned above. Your scoring table can be based on any property you feel is appropriate. Show your scoring table* in a Word document named Table_HW4.doc and explain the reasoning behind the values in the scoring table you developed. Show the salmon vs mosquito alignment in your GI notebook when using your table in GI_HW4.nbk. How does it compare to the alignments you got in part 1? Why are there differences?

Part 3: Multiple Alignments 40 points

Align all of the trypsin sequences in a multiple sequence alignment using your new table. Click on a sequence name and then choose Select-All [command-A (Mac)|control-A (Windows)] and drag the selected sequence alignment to your GI notebook, GI_HW4.nbk. Try a couple of alignments using standard tables, and place those in the notebook as well. Does your table bring out some interesting features? How does it compare with standard tables used in an alignment? Discuss this in your notebook.

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* You can open the table editor in GI, select all, then copy the table to the clipboard. Next, open Word and paste in the text. Finally, select the text (table) you just pasted in and convert it to a table using the TABLE > CONVERT > CONVERT TEXT TO TABLE menu option.