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

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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 about the Sfold algorithm?

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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. 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.

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