RNA Structure Prediction

This quiz contains multiple-choice problems on RNA structures, RNA genomes, RNA structure modelling applications, RNA secondary structure prediction methods, ab initio and comparative approach, performance evaluation, prediction limitations, energy method and free grammars.

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RNA structures can be experimentally determined using

X-ray crystallography techniques only

NMR techniques only

X-ray crystallography or NMR techniques

Gel electrophoresis

Which of the following is not a form of RNA?

mRNA

tRNA

qRNA

rRNA

Unlike DNA, which is mainly double-stranded, RNA is double-stranded, although an RNA molecule can self-hybridize at certain regions to form partial double-stranded structures. True or false?

True

False

Structures are not very important when it comes to the study of functions. True or false?

True

False

Which of the following is not an RNA base?

Thymine (T)

Adenine (A)

Cytosine (C)

Guanine (G)

Base pairing in RNA is A–G and U–C. True or false?

True

False

In addition to the canonical base pairing, non-canonical base pairings often exist, such as __ and __ base paring.

G, U

G, C

U, C

A, C

Four main subtypes of secondary structures can be identified. They are hairpin loops, bulge loops, interior loops, and multi-branch loops. True or false?

True

False

The __ refers to a structure with two ends of a single-stranded region (loop) connecting a base-paired region (stem).

Helical junctions

Hairpin loop

Bulge loop

Interior loop

The __ refers to two single-stranded regions connecting two adjacent base-paired segments on opposite strands.

Hairpin loop

Interior loop

Pseudoknot loop

Helical junctions

Which of the following is true about the RNAalifold?

Dynamic programming is not involved

Minimum free energy method is not used

Only minimum free energy is used

Covariation information is taken into consideration

The predefined alignment requiring method also depends on the quality of the input alignment. If there __ errors in the alignment, covariation signals __ detected.

are, will be

are, will not be

are not, will not be

are not, possibly will not be

The type of algorithm that __ predefined alignment is __ for reasonably conserved sequences.

does not require, more successful

requires, less successful

does not require, relatively successful

requires, relatively successful

The type of algorithm that requires predefined alignment requires the user to provide __ alignment as input.

Not necessarily an alignment

Multiple only