Q. The Second assumption in predicting RNA secondary structure is that the energy associated with any position in the structure is _____ influenced by local sequence and structure.

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Q. The third assumption in predicting RNA secondary structure is that the structure is assumed to be formed by _____ of the chain back on itself in a manner that ________

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Q. Martinez (1984) made a list of possible double-stranded regions, and these regions were then given weights in proportion to their equilibrium constants, calculated by ______

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Q. In 1971, first estimation of the energy associated with regions of secondary structure by extrapolation from studies with small molecules was done and then an attempt was made to predict which configurations of larger molecules were the most energetically stable.

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Q. Nussinov and Jacobson (1980) were the first to design a precise and efficient algorithm for predicting secondary structure.

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Q. Which of the following is incorrect about the prediction of RNA secondary structure?

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Q. Through a single scoring matrix, evaluation of all the different possible configurations is done.

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Q. The object is to find a diagonal row of matches that goes from upper left to lower right.

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Q. The increase depends on the type and length of loop that is introduced by the non-complementary base pair, whether internal loop, bulge loop, or hairpin loop.

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Q. The sequence is listed down the first column of base comparisons’ table and free energy calculations’ table in the 5’→3’ orientation.

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Q. A general theory for modeling strings of symbols, such as bases in DNA sequences, has been developed by linguists. There is a hierarchy of these so-called transformational grammars that deal with situations of increasing complexity.

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Q. ______ regions in sequences, such as those in RNA that will form secondary structures, are an example of such context-free sequences.

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Q. The use of SCFGs in RNA secondary structure production analysis is in fact very similar to that of the covariance model, with the grammatical productions resembling the nodes in the ordered binary tree.

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Q. In a SCFG, each production of a non-terminal symbol has an associated probability for giving rise to the resulting product, and there are a set of productions, each giving a different result.

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Q. The application of SCFGs to RNA secondary structure analysis is very similar in form to the probabilistic covariance models.

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

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

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

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Q. 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.

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

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