Ab Initio Approach MCQs : This section focuses on the "Ab Initio Approach". These Multiple Choice Questions (MCQs) should be practiced to improve the Ab Initio Approach skills required for various interviews (campus interview, walk-in interview, company interview), placement, entrance exam and other competitive examinations.
Question 1
In ab initio methods, a quantitative approach such as dynamic programming can be used to assemble a final structure with optimal base-paired regions.
A. True
B. False
Question 2
In dot matrix in ab initio methods, one way to reduce the noise in the matrix is to select an appropriate window size of a maximum number of contiguous base matches.
A. True
B. False
Question 3
In dot matrix in ab initio methods, the diagonals _____________ to the main diagonal represent regions that can self hybridize.
A. parallel
B. cutting in random fashion
C. perpendicular
D. adjacent parallel
Question 4
In dynamic programming, in ab initio methods, Often ________ base pairing and energy terms of the base pairing _____ incorporated into the scoring process.
A. G-C, are
B. G–U, are not
C. G–U, are also
D. G-C, are not
Question 5
In dynamic programming, in ab initio methods, the use of a dot plot can be effective in finding a ____ secondary structure in a ________ molecule.
A. multiple, large
B. single, large
C. single, small
D. multiple, small
Question 6
Like Mfold, RNAfold only examines the energy terms of the optimal alignment in a dot plot.
A. True
B. False
Question 7
The dynamic programming method produces ____ structure with _____ score.
A. one, single best
B. multiple, single best
C. multiple, multiple
D. single, multiple
Question 8
The problem of dynamic programming to select one single structure can be complemented by adding a probability distribution function, known as the _________ which calculates a mathematical distribution of probable base pairs in thermodynamic equilibrium.
A. partition function
B. division function
C. increment function
D. fold function
Question 9
Which of the following about the RNAFold is incorrect?
A. It extends the sequence alignment to the vicinity of the optimal diagonals to calculate thermodynamic stability of alternative structures
B. It incorporates a partition function
C. It doesn’t necessarily use a partition function
D. It aims to select a number of statistically most probable structures in one of its steps
Question 10
Which of the following is correct about MFOLD?
A. It uses the dynamic programming only
B. It uses the thermodynamic calculations only
C. It uses the both dynamic programming and thermodynamic calculations as well
D. It doesn’t take into account the themoststablility of the secondary structures