Q. Ab initio methods are energetically least favorable.

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Q. The dot matrix method and the dynamic programming method can be used in detecting self-complementary regions of a sequence.

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Q. In dot matrix in ab initio methods, the diagonals _____________ to the main diagonal represent regions that can self hybridize.

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Q. 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.

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Q. In dynamic programming, in ab initio methods, the use of a dot plot can be effective in finding a ____ secondary structure in a ________ molecule.

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Q. In ab initio methods, a quantitative approach such as dynamic programming can be used to assemble a final structure with optimal base-paired regions.

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Q. In dynamic programming, in ab initio methods, Often ________ base pairing and energy terms of the base pairing _____ incorporated into the scoring process.

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Q. The dynamic programming method produces ____ structure with _____ score.

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Q. 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.

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Q. Which of the following is correct about MFOLD?

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

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Q. Which of the following about the RNAFold is incorrect?

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Q. In ab initio methods for RNA structure prediction, the prediction results from RNAfold are not always guaranteed to be better than those predicted by Mfold.

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Q. The comparative approach uses basic RNA structure based predictions to infer a consensus structure.

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Q. To distinguish the conserved secondary structure among multiple related RNA sequences, a concept of “covariation” is used.

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Q. ___________ of covariation can be ___________ to the RNA structure and functions.

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Q. An aspect of the comparative method is to select a __________ structure through consensus drawing.

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Q. The comparative-based algorithms can be further divided into two categories based on the type of input data.

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Q. The type of algorithm that requires predefined alignment, requires the user to provide _______ alignment as input.

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Q. The type of algorithm that _____ predefined alignment is ______ for reasonably conserved sequences.

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