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.

View solution

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.

View solution

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?

View solution

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?

View solution

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?

View solution

Q. The program may be instructed to find structures within a certain percentage of the minimum free energy.

View solution

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.

View solution

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

View solution

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

View solution

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

View solution

Q. The application of SCFGs to RNA secondary structure analysis is very similar in form to the probabilistic covariance models.

View solution

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.

View solution

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.

View solution

Q. ______ regions in sequences, such as those in RNA that will form secondary structures, are an example of such context-free sequences.

View solution

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.

View solution

Q. The sequence is listed down the first column of base comparisons’ table and free energy calculations’ table in the 5’→3’ orientation.

View solution

Q. The increase depends on the type and length of loop that is introduced by the non-complementary base pair, whether internal loop, bulge loop, or hairpin loop.

View solution

Q. The object is to find a diagonal row of matches that goes from upper left to lower right.

View solution

Q. Through a single scoring matrix, evaluation of all the different possible configurations is done.

View solution

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

View solution