Bioinformatics Mcqs

Page No. 44

Three sc is the total number of energy dots regardless of color in the i th row and i th column of the energy dot plotores, Pnum (i), Hnum (i,j), and Ssum, have been derived to assist with a determination of the reliability of a secondary structure prediction for a particular base i or a base pair i,j. Which of the following is not a correct regarding Pnum?


a is the total number of energy dots regardless of color in the i th row and i th column of the energy dot plot


bis the total number of energy dots considering the color in the ith row and ith column of the energy dot plot


c represents in an unfiltered dot plot


d represents the number of base pairs



The program may be instructed to find structures within a certain percentage of the minimum free energy.


aTrue


b False


ceither true and false


dnone of these


View Answer True

In the programs related to FOLD, All complementary base pairs can be sampled in a fashion to determine which are present in a suboptimal structure.


aTrue


bFalse


ceither true and false


dnone of these


View Answer True

In the programs related to FOLD, the second region, the ________ region, is used to calculate the energy of the ________ structure.


aincluded, most likely


b included, best


cexcluded, least likely


d excluded, best


View Answer excluded, best

To find suboptimal structures, the dynamic programming method was modified.


a True


bFalse


ceither true and false


dnone of these


View Answer True

Originally, the FOLD program of _____ predicted _____ having the minimum free energy.


aM. Zuker, two structures


bM. Wunsch, two structures


cM. Zuker, only one


dM. Wunsch, only one


View Answer M. Zuker, only one

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.


aTrue


b False


ceither true and false


dnone of the mentioned


View Answer True

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.


aTrue


b False


ceither true and false


dnone of the mentioned


View Answer True

Which of the following is untrue about the Sfold algorithm?


aIt uses a unique algorithm to aid in the design of siRNA


bThe algorithm combines thermodynamic stabilities, calculations of target accessibility, and empirical rules


cThe website offers specialized programs for the design of siRNA, antisense RNA, trans-cleaving RNA, and mRNA-microRNA interactions


dThe website doesn’t offer programs for the design of a general program for statistically sampling suboptimal RNA structures



Which of the following is untrue about Vienna RNA Websuite?


aIt introduced the Wuchty algorithm, developed applications of the McCaskill algorithm


bIt also offers a wide variety of algorithms and functions


cThe Wuchty algorithm generates a small but complete set of suboptimal structures


dThe Wuchty algorithm computes some possible tertiary structures within a narrow free-energy range



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