Questions and answers for exam Preparation

MCQs

Total Questions : 90 | Page 4 of 9 pages

Question 31. The dynamic programming method produces ____ structure with _____ score.

one, single best
multiple, single best
multiple, multiple
single, multiple

Discuss Question

Answer: Option A. -> one, single best
Answer: (a).one, single best

Question 32. Which of the following about the RNAFold is incorrect?

It extends the sequence alignment to the vicinity of the optimal diagonals to calculate thermodynamic stability of alternative structures
It incorporates a partition function
It doesn’t necessarily use a partition function
It aims to select a number of statistically most probable structures in one of its steps

Discuss Question

Answer: Option C. -> It doesn’t necessarily use a partition function
Answer: (c).It doesn’t necessarily use a partition function

Question 33. Which of the following is correct about MFOLD?

It uses the dynamic programming only
It uses the thermodynamic calculations only
It uses the both dynamic programming and thermodynamic calculations as well
It doesn’t take into account the themoststablility of the secondary structures

Discuss Question

Answer: Option B. -> It uses the thermodynamic calculations only
Answer: (b).It uses the thermodynamic calculations only

Question 34. Like Mfold, RNAfold only examines the energy terms of the optimal alignment in a dot plot.

True
False
May be True or False
Can't say

Discuss Question

Answer: Option B. -> False
Answer: (b).False

Question 35. 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.

partition function
division function
increment function
fold function

Discuss Question

Answer: Option A. -> partition function
Answer: (a).partition function

Question 36. Which of the following is untrue regarding RNA structure?

RNA structure 4.6 is a Windows implementation of the Zuker algorithm
It includes additional options for other folding algorithms and incorporation of experimental data
The authors of RNA structure collaborate very closely with the Turner laboratory and keep the most up-to-date thermodynamic parameters
The OligoWalk program cannot be used for siRNA design

Discuss Question

Answer: Option D. -> The OligoWalk program cannot be used for siRNA design
Answer: (d).The OligoWalk program cannot be used for siRNA design

Question 37. The ILM program uses an iterative loop matching algorithm to maximize base pairs and allows pseudoknots to form by allowing base. pairs to be added or removed in successive rounds.

True
False
May be True or False
Can't say

Discuss Question

Answer: Option A. -> True
Answer: (a).True

Question 38. Which of the following is untrue about the Sfold algorithm?

It uses a unique algorithm to aid in the design of siRNA
The algorithm combines thermodynamic stabilities, calculations of target accessibility, and empirical rules
The website offers specialized programs for the design of siRNA, antisense RNA, trans-cleaving RNA, and mRNA-microRNA interactions
The website doesn’t offer programs for the design of a general program for statistically sampling suboptimal RNA structures

Discuss Question

Answer: Option D. -> The website doesn’t offer programs for the design of a general program for statistically sampling suboptimal RNA structures
Answer: (d).The website doesn’t offer programs for the design of a general program for statistically sampling suboptimal RNA structures

Question 39. If the centroid structure is different from the minimum free-energy structure, the centroid structure is often closer to the phylogenetic prediction and contains fewer base pairs, or fewer false-positive base pair predictions, than the minimum free-energy prediction.

True
False
May be True or False
Can't say

Discuss Question

Answer: Option A. -> True
Answer: (a).True

Question 40. Which of the following is untrue about Vienna RNA Websuite?

It introduced the Wuchty algorithm, developed applications of the McCaskill algorithm
It also offers a wide variety of algorithms and functions
The Wuchty algorithm generates a small but complete set of suboptimal structures
The Wuchty algorithm computes some possible tertiary structures within a narrow free-energy range

Discuss Question

Answer: Option D. -> The Wuchty algorithm computes some possible tertiary structures within a narrow free-energy range
Answer: (d).The Wuchty algorithm computes some possible tertiary structures within a narrow free-energy range