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Bioinformatics Practice Test Questions: RNA Structure Prediction
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RNA structure prediction is a method that aims to predict the base-pairing structure of a given RNA sequence. The most common approach for predicting RNA secondary structures is based on thermodynamic models. These models decompose a secondary structure into substructures, called nearest-neighbor loops. Topics include: Types of RNA Structures, RNA Secondary Structure Prediction Methods, Ab Initio Approach, Comparative Approach, Performance Evaluation, Limitations of Prediction, Minimum Free – Energy Method & Stochastic Context – Free Grammars, MFOLD and the Use of Energy... Show more
Bioinformatics Practice Test Questions: RNA Structure Prediction
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25 Questions

1. Fichant and Burks (1991) described a program, tRNAscan, that searches a genomic sequence with a sliding window searching simultaneously for matches to a set of invariant bases and conserved self-complementary regions in tRNAs with an accuracy of 97.5%.
2. The __________ refers to two single-stranded regions on opposite strands connecting two adjacent base-paired segments.
3. ______ regions in sequences, such as those in RNA that will form secondary structures, are an example of such context-free sequences.
4. An aspect of the comparative method is to select a __________ structure through consensus drawing.
5. The pre-alignment independent programs fare __________ for predicting long sequences.
6. In comparative approach to RNA structure prediction, Foldalign is a web-based only program for RNA alignment
7. 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.
8. Originally, the FOLD program of _____ predicted _____ having the minimum free energy.
9. Ab initio approach makes structural predictions based on ______
10. The comparative approach uses basic RNA structure based predictions to infer a consensus structure.
11. Which of the following is not a base of RNA?
12. In 1971, first estimation of the energy associated with regions of secondary structure by extrapolation from studies with small molecules was done and then an attempt was made to predict which configurations of larger molecules were the most energetically stable.
13. If the centroid structure is different from the minimum free-energy structure, the centroid structure is often closer to the phylogenetic prediction and contains fewer base pairs, or fewer false-positive base pair predictions, than the minimum free-energy prediction.
14. In comparative approach to RNA structure prediction, the Foldalign program doesn’t use the covariation information.
15. 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 ________
16. RNA secondary structure is composed primarily of triple-stranded RNA regions formed by folding the single-stranded molecule back twice on itself.
17. The program may be instructed to find structures within a certain percentage of the minimum free energy.
18. At present, there are essentially two types of method of RNA structure prediction. One is the minimum free energy approach and the Second one is a comparative approach.
19. In ab initio methods, free energy can be calculated based on parameters empirically derived for small molecules.
20. 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.
21. Which of the following is incorrect about the RNA structure prediction?
22. In comparative approach to RNA structure prediction, Dynalign is a ________ program.
23. Rigorously evaluating the performance of RNA prediction programs has traditionally been hindered by the dearth of three-dimensional structural information for RNA.
24. Nussinov and Jacobson (1980) were the first to design a precise and efficient algorithm for predicting secondary structure.
25. 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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