Q. The predefined alignment requiring method also depends on the quality of the input alignment. If there ___ errors in the alignment, covariation signals ____ detected.

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Q. Which of the following is true about the RNAalifold?

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Q. Rigorously evaluating the performance of RNA prediction programs has traditionally been hindered by the dearth of three-dimensional structural information for RNA.

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Q. If prediction accuracy can be represented using a ______ the ______ programs score roughly 20% to 60% depending on the length of the sequences.

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Q. For _________ RNA sequences, such as tRNA, some programs may be able to produce _________% accuracy.

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Q. The pre-alignment independent programs fare __________ for predicting long sequences.

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Q. Based on recent benchmark comparisons, the comparative-type algorithms can reach an accuracy range of 20% to 80%.

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Q. In comparative approach to RNA structure prediction, algorithms that do not use pre-alignment, align multiple input sequences and infers a consensus structure.

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Q. In comparative approach to RNA structure prediction, Foldalign is a web-based only program for RNA alignment

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Q. In comparative approach to RNA structure prediction, the Foldalign program doesn’t use the covariation information.

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Q. In comparative approach to RNA structure prediction, Dynalign is a ________ program.

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Q. In comparative approach to RNA structure prediction, in Dynalign program–by comparing _________ from each sequence, a ______ structure common to both sequences is selected that serves as the basis for sequence alignment.

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

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Q. A type of RNA secondary structure prediction method takes into account conserved patterns of base-pairing that are conserved during evolution of a given class of RNA molecules.

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Q. RNA secondary structure is composed primarily of triple-stranded RNA regions formed by folding the single-stranded molecule back twice on itself.

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Q. ____ wobble pairs may be produced in these double-stranded regions.

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Q. In predicting RNA secondary structure, some simplifying assumptions are usually made, like the _____ structure is similar to the _____

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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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