What is the measure of confidence used for phylogenetic tree construction?

BIFS 614 Data Structure and Algorithms – Final Exam

Dr. Wolfgang Rumpf

Due to the sensitive nature of final exams, you must turn this in on time. Failure to do so will results in a loss of one letter grade per day late.

1. Given the following sequence from Saccharomyces cerevisease: GATCTCACGATATAT

a. What is the most likely translation frame? (10 points)

b. What is this sequence? How can you tell? (10 points)

2. Given the following DNA sequence: GGTGTAAAGAATCTT

a. Construct a keyword tree (10 points)

b. Construct a suffix tree (10 points)

3. Given the following distance matrix, construct a neighbor-joining distance tree. Show all your work! (20 points).

4. Describe in detail how the BLAST algorithm works (10 points).

5. What are the criteria for confidence for the strength of a BLAST hit? (5 points).

6. What is the measure of confidence used for phylogenetic tree construction? (5 points)

7. What is meant by “wobble” in reference to the genetic code? (5 points)

8. How many different nucleotide sequences can code for the following protein sequence: (15 points): Arg-Lys-Pro-Val-Ser-Ile-Ala

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