Bioinformatics Mcqs

Page No. 43

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.


aTrue


bFalse


ceither true and false


dnone of these


View Answer True

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


aTrue


bFalse


ceither true and false


dnone of these


View Answer True

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.


aTrue


bFalse


ceither true and false


dnone of these


View Answer True

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


a True


b False


ceither true and false


dnone of these


View Answer False

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


a True


bFalse


ceither true and false


dnone of these


View Answer False

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


aEvery base is first compared to every other base by a type of analysis very similar to the dot matrix analysis


b A row of matches in the RNA matrix indicates a succession of complementary nucleotides that can potentially form a double-stranded region


cA row of matches in the RNA matrix indicates a failure of complementary nucleotides that can potentially form a double-stranded region


dThe sequence is listed across the top and down the side of the page, and G/C, A/U, and G/U base pairs are scored



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.


aTrue


b False


ceither true and false


dnone of these


View Answer True

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


bFalse


ceither true and false


dnone of these


View Answer True

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?


ais also called as ss-count


bis the number of foldings in which base i is single-stranded divided by m, the number of folding


cis the number of foldings in which base i is single-stranded multiplied by m, the number of folding


dgives the probability that base i is single-stranded



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?


ais the sum of Pnum(i) and Pnum(j) -1


b is the sum of Pnum(i) and Pnum(j) + 1


cis the total number of dots in the ith row and jth column


drepresents the total number of base pairs with the ith or jth base in the predicted structures



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