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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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. 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 Ssum?

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

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

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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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