HW5 - 1.) Do problem 6.9 from the Supplement. Choose...

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Chem 476 HW 5 Due Oct 3, 2007 “BLAST!” Name:________________________ Please complete all questions. Do your work on additional sheets of paper and staple to the back of this sheet. Do not put your answers on this page. You may work with your classmates on this and all homework assignments. I will grade the same three questions for all students and post the answers to the questions after they are due. I.) Problems from the textbook and supplement (do not hand in). Answers are in the textbook (short answers) and supplement (full answers to text AND supplement), but work through on your own first. : Text: 5.1, 5, 9; 6.1, 3, 7, 10. (many of these are short answer) Supp: 6.1-3, 6-8. II.) Additional Problems to hand in : The goal of this exercise is to get you some experience using the BLAST comparison software. Both of these problems are from the Problems section of Chapter 6 in the Supplement.
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Unformatted text preview: 1.) Do problem 6.9 from the Supplement. Choose Chicken for your organism. Answer the following questions. a.) Print out and attach results of your BLAST. You should have 3 sequences. b.) Define the following terms or symbols: Query: Sbjct: Expect (and what does a very low score mean): + symbol: Identities: Positives: Gaps: Gallus gallus: c.) What is the name and function of the protein with most similar match? d.) What is the FULL sequence of the most similar match? (Hint: you will have to do something not described in the Supplement). You can just paste it here. e.) Using the rules of thumb, how would you estimate relatedness of these two proteins? f.) What similarity matrix was used by BLAST? (You can find it on the output page). 2.) Do problem 6.10 parts a and b from the Supplement. For each problem give the name of the protein and paste the entire sequence of the Sbjct below....
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This note was uploaded on 07/23/2008 for the course CHEM 476 taught by Professor Bevilacqua,philip during the Fall '07 term at Pennsylvania State University, University Park.

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HW5 - 1.) Do problem 6.9 from the Supplement. Choose...

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