1. If you want to align 2 DNA sequences you can use many different substitution

Question

1. If you want to align 2 DNA sequences you can use many different substitution matrices. PAM 250 and Blosum 62 Matrices are two good choices.
True
False

2. In the case of closely related sequences a BLOSUM 62 matrix should yield more significant matches than a BLOSUM 50 matrix.
True
False

3. One way to root a phylogenetics tree is to include a sequence from a closely related group.
True
False

4. When you used blast to explore the protein function of one of the candidate virulence factor (in chapter 5) you also got access to conserved domain information present in the input sequence. This information is included in each blast search since all proteins have conserved functional domain.
True
False

5. In a phylogenetic tree an internal node correspond to the last common ancestor of a clade.
True
False

6. Which sentence is true.
A. The number 20 in a PAM 20 matrix indicates the presence of 20 mutations per 100 residues. This mean 1 mutation for 20 different amino acids in a sequences of 100 residues.  
B. BLOSUM matrices were build using global alignment of conserved blocks of amino acids.  
C. In a BLOSUM matrix a positive score mean an observed substitution. A higher number means that this substitution is less probable to happen by chance.  
D. If you use a PAM or BLOSUM matrix, gaps will not be allowed in your alignment and will receive a score of 0.   Reset Selection

7. The Jukes -Cantor model _____
A. estimates the number of substitutions between sequences since they last shared a common ancestor.  
B. take into account the transversions only.  
C. Will always only show a linear increase in distance as number of substitutions increases.  
D. is an algorithm used to build phylogenetic trees  

8. Transversion mutations ______
A. are more common than transitions  
B. change a purine for a pyrimidine or a pyrimidine for a purine.  
C. cannot affect the function of a protein  
D. are not substitutions since they are a the DNA level.

Explanation / Answer

1.False

2.False

3.True

4.False

5. D. If you use a PAM or BLOSUM matrix, gaps will not be allowed in your alignment and will receive a score of 0.

6. C. In a BLOSUM matrix a positive score mean an observed substitution. A higher number means that this substitution is less probable to happen by chance.

7. B. take into account the transversions only.  

8. A. are more common than transitions

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