Which of the following is true regarding the assumptions in the method of constructing the Dayhoff scoring matrix?

it is assumed that each amino acid position is not equally mutable

it is assumed that each amino acid position is equally mutable

it is assumed that each amino acid position is not equally mutable

it is assumed that each amino acid position is not mutable at all

sites do not vary in their degree of mutability

Which of the following doesn t describe PAM matrices?

This family of matrices lists the likelihood of change from one amino acid to another in homologous protein sequences during evolution

There is presently no other type of scoring matrix that is based on such sound evolutionary principles as are these matrices

Even though they were originally based on a relatively small data set, the PAM matrices remain a useful tool for sequence alignment

It stands for Percent Altered Mutation

Explore topic-wise MCQs in Bioinformatics.

This section includes 6 Mcqs, each offering curated multiple-choice questions to sharpen your Bioinformatics knowledge and support exam preparation. Choose a topic below to get started.

1.	In case of the varying alignment, penalizing gaps heavily might occur. Then the best scoring local alignment between the sequences will be one that optimizes the score between matches and mismatches, without any gaps.
A.	True
B.	False
Answer» B. False

Discussion

2.	In the GCG and FASTA program suites, the scoring matrix itself is formatted in a way that includes default ______
A.	gap additions
B.	alignment scores
C.	score penalties
D.	gap penalties
Answer» E.

Discussion

3.	A gap opening penalty for any gap (g) and a gap extension penalty for each element in the gap (r) are most often used, to give a total gap score wx, according to the equation ______
A.	wx rx = -g
B.	wx = g rx
C.	wx = g + rx
D.	wx + g + rx = 0
Answer» D. wx + g + rx = 0

Discussion

4.	Which of the following is true regarding the assumptions in the method of constructing the Dayhoff scoring matrix?
A.	it is assumed that each amino acid position is equally mutable
B.	it is assumed that each amino acid position is not equally mutable
C.	it is assumed that each amino acid position is not mutable at all
D.	sites do not vary in their degree of mutability
Answer» B. it is assumed that each amino acid position is not equally mutable

Discussion

5.	Which of the following doesn t describe PAM matrices?
A.	This family of matrices lists the likelihood of change from one amino acid to another in homologous protein sequences during evolution
B.	There is presently no other type of scoring matrix that is based on such sound evolutionary principles as are these matrices
C.	Even though they were originally based on a relatively small data set, the PAM matrices remain a useful tool for sequence alignment
D.	It stands for Percent Altered Mutation
Answer» E.

Discussion

6.	In scoring matrices, for convenience, odds scores are converted to log odds scores.
A.	True
B.	False
Answer» B. False

Discussion

Explore topic-wise MCQs in Bioinformatics.

In case of the varying alignment, penalizing gaps heavily might occur. Then the best scoring local alignment between the sequences will be one that optimizes the score between matches and mismatches, without any gaps.

In the GCG and FASTA program suites, the scoring matrix itself is formatted in a way that includes default ______

A gap opening penalty for any gap (g) and a gap extension penalty for each element in the gap (r) are most often used, to give a total gap score wx, according to the equation ______

Which of the following is true regarding the assumptions in the method of constructing the Dayhoff scoring matrix?

Which of the following doesn t describe PAM matrices?

In scoring matrices, for convenience, odds scores are converted to log odds scores.