There are two parts to this homework.
1. Choose either part 1A part 1B - do NOT do both parts. (50 points)
- A. Fill in a dynamic programming grid. Download the needed files by clicking here. This archive contains two Excel files: a spread sheet with a PAM250 table and a spread sheet with a dynamic programming grid to be filled in. Fill in the numbers directly on the computer (in Excel) and hand in the filled in grid. Also indicate the appropriate traceback through the grid for the best global alignment (used colored text in the cells on the optimal path) and show the alignment (use courier font and another cell(s) on the same spreadsheet to hold the alignment). Rename the spreadsheet as dynamic_programming_HW5.xls
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- B. This option is mostly for the Computer Science majors in the class. Write a dynamic programming demo program like the Hypercard Stack shown in class. It should include the ability to use scoring tables, define gap penalties, trace back through the matrix, and show alignments. If you choose this option, you must come to see me first for permission - I'd like to make sure you can actually do the project and I want to work on the interface with you. Also, this project will not have to be handed in within a week.
2. Using BLAST and/or PSI-BLAST searches define the relationship among the following enzymes. Put all your research results (graphics, text discussion, etc.) about the comparisons in a word document called blast_HW5.doc, and hand that document in. You should restrict your search to looking in just FUNGI by using the text field in the "organism" section of the protein BLAST page. In your analysis be sure to look at the list of hits you get in your database searches and think about identifying the locations of those matches in the various sequences. You might benefit from combining the sequences and doing a search. Describe the relationship among the proteins and compare this to what you might find in some other species for these proteins. (50 points)
- 3-Dehydroquinate synthase Accession#Q9PK25
- Shikimate 5-dehydrogenase Accession#BAA15449
- 3-Phosphoshikimate 1-carboxyvinyl transferase (5-enolpyruvulshikimate-3-phosphate synthase)(EPSP SYNTHASE) (EPSPS) Accession#P52312
What to Hand In
Place your two documents into a single folder called lastname_firstname_HW5 and stuff (or zip) the folder and then hand that stuffed/zipped file in through the Blackboard system.