Q. 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.

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Q. Which of the following is untrue about the Sfold algorithm?

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

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Q. Which of the following is untrue regarding RNA structure?

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Q. The probability model mentioned above was a hybrid combination of HMMs and SCFGs trained on sno RNAs.

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Q. The probabilistic model was used to identify small nucleolar (sno) RNAs in the yeast genome that methylate ribosomal RNA.

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Q. Fichant and Burks (1991) described a program, tRNAscan, that searches a genomic sequence with a sliding window searching simultaneously for matches to a set of invariant bases and conserved self-complementary regions in tRNAs with an accuracy of 97.5%.

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Q. One of the first methods used to find tRNA genes was to search for sequences that are complementary and can fold into a knot like the three found in tRNAs.

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Q. ______ molecules can simply be identified based on their sequence similarity with already-known sequences.

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Q. These limitations of the Zuker method and other methods have been largely overcome by using an algorithm originally described by Waterman and Byers (1985) for finding sequence alignments within a certain range of the optimal one by modifications of the trace-back procedure used in dynamic programming.

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Q. A limitation of the Zuker method and other methods (Nakaya et al. 1995) for computing suboptimal RNA structures is that they do not compute all the structures within a given energy range of the minimum free-energy structure.

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Q. Three scores, 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 Ssum?

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Q. Three scores, 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 Hnum?

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Q. Three scores, 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?

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

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

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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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