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.

A limitation of the Zuker method and other methods (Nakaya et al. 199

1.	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.
A.	True
B.	False
Answer» B. False

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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.
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.
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?
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?
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?
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.
In the programs related to FOLD, the second region, the ________ region, is used to calculate the energy of the ________ structure.
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.?$
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.$
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.

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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