Which of the following is incorrect about the prediction of RNA secondary structure?(a) Every 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(c) A row of matches in the RNA matrix indicates a failure of complementary nucleotides that can potentially form a double-stranded region(d) The sequence is listed across the top and down the side of the page, and G/C, A/U, and G/U base pairs are scoredThis question was posed to me in homework.My question is taken from Minimum Free in division RNA Structure Prediction of Bioinformatics

Which of the following is incorrect about the prediction of RNA second

1.	Which of the following is incorrect about the prediction of RNA secondary structure?(a) Every 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(c) A row of matches in the RNA matrix indicates a failure of complementary nucleotides that can potentially form a double-stranded region(d) The sequence is listed across the top and down the side of the page, and G/C, A/U, and G/U base pairs are scoredThis question was posed to me in homework.My question is taken from Minimum Free in division RNA Structure Prediction of Bioinformatics
Answer» Correct option is (c) A ROW of matches in the RNA MATRIX INDICATES a failure of COMPLEMENTARY nucleotides that can potentially form a double-stranded region Explanation: The energy of each predicted structure is estimated by the nearest- neighbor rule by summing the NEGATIVE base-stacking energies for each pair of bases in double-stranded regions. By adding the estimated positive energies of destabilizing regions such as loops at the end of hairpins, bulges within hairpins, internal bulges, and other unpaired regions.

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