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The correct choice is (a) True

Explanation: The point is to show a structure that REPRESENTS a GROUP of structures rather than a single predicted structure. Many long RNA sequences, such as viral genomes or MRNA, may not have a single structure but instead have a dynamic structure that has some conserved features but also varies and CHANGES, and these many conformations may all EXIST simultaneously in the cell.

Right option is (a) True

For explanation I would say: This method efficiently CALCULATES a large number of alternative STRUCTURES, up to a very large number, within a given energy range of the MINIMUM free-energy structure. The method has been used to DEMONSTRATE that natural tRNA sequences can form many alternative structures that are close to the minimum free-energy structure and that base modification plays a major role in this ENERGETIC stability.

Correct option is (b) Larger, highly conserved

The best explanation: For smaller sequences with more sequence variation, this method does not WORK. A NUMBER of METHODS for finding small RNA genes have been described and are available on the Web. A major PROBLEM with these methods in searches of large genomes is that a small false positive rate becomes quite unacceptable because there are so MANY false positives to check out.

Correct option is (b) False

The best EXPLANATION: One of the first methods used to find tRNA genes was to SEARCH for sequences that are self-complementary and can fold into a HAIRPIN like the three found in tRNAs (Staden 1980). Through the regions of self-complimentarity it was first possible to find the tRNA.

Correct answer is (a) True

To elaborate: A method for FINDING the RNA polymerase III transcriptional control regions of tRNA genes using a scoring matrix derived from known control regions, was derived. That is also very accurate. Finally, Lowe and Eddy (1997) have devised a search ALGORITHM tRNAscan-SE that uses a combination of THREE methods to find tRNA genes in genomic sequences—tRNAscan, the Pavesi algorithm, and the COVELS program based on sequence COVARIANCE analysis (Eddy and Durbin 1994). This method is reportedly 99–100% accurate with an extremely low rate of FALSE positives.

Right answer is (d) The Wuchty algorithm computes some possible TERTIARY structures within a narrow free-energy range

The explanation is: The Wuchty algorithm computes all possible secondary structures within a narrow free-energy range. The Wuchty algorithm generates a small but complete set of suboptimal structures that may INCLUDE some very different secondary structures but also very many HIGHLY similar structures. However, structures containing more than one suboptimal region may occur in the Wuchty set of structures but would be absent if the Zuker METHOD for sampling suboptimal structures were used.

The correct CHOICE is (d) The website doesn’t offer programs for the design of a general program for statistically sampling suboptimal RNA STRUCTURES

Easy EXPLANATION: The algorithm uses a partition function calculation and then groups suboptimal structures by similarity. The centroid structure is the most-representative structure that is closest in similarity to all the other structures.

Correct CHOICE is (a) True

The explanation is: The model is not used to SEARCH genomic sequences DIRECTLY. Instead, a list of candidate sequences is first found by searching for PATTERNS that MATCH the sequences in the model (Lowe and Eddy 1999).

Right option is (a) True

The explanation: For example, no alternative structures are produced that have the absence of BASE pairs in the best structure, and, if two SUBSTRUCTURES are joined by a stretch of UNPAIRED bases, no structures are produced that are suboptimal for both structures. These FACTORS limit the number of alternative structures predicted compared to known VARIATIONS based on sequence variations in tRNAs.

Right OPTION is (d) The OligoWalk program cannot be USED for SIRNA design

The best explanation: Two unique WAYS of incorporating experimental data in the RNA folding is done with Dynalign and chemical modification. The Dynalign program computes the lowest free-energy sequence alignment and secondary structure COMMON to two RNA sequences.

The CORRECT ANSWER is (a) True

The BEST I can explain: These RNAs vary SUFFICIENTLY in sequence and structure that they are not found by straightforward similarity SEARCHES. The RNAs found were shown to be sno RNAs by insertional mutagenesis.

The CORRECT choice is (B) is the sum of Pnum(i) and Pnum(j) + 1

The explanation: The Hnum for a double stranded REGION is the average Hnum value for the BASE pairs in that helix. The LOWER this number, the more well determined the double-stranded region.

The correct choice is (b) is the TOTAL NUMBER of energy dots considering the color in the ith row and ith COLUMN of the energy dot plot

The best explanation: It represents the number of base pairs that the ith base can form with all other base pairs in STRUCTURES WITHIN the defined energy range. The lower this value, the better defined or “well determined” the local structure because there are few competitive foldings.

The CORRECT choice is (a) True

The best I can explain: This comparison of all possible matches and energy values is CONTINUED until all nucleotides have been compared. There is a pattern followed in comparing bases within the RNA MOLECULE.

The correct option is (b) the Boltzmann function [exp (-∆G/RT)]

For explanation: Here, the (-∆G) is the FREE energy of the regions, R is the gas constant, and T is the temperature. The RNA MOLECULE is FOLDED by a Monte Carlo method in which one initial REGION is chosen at RANDOM from a weighted pool, similar to the method used in Gibbs sampling.

The correct option is (d) folding, does not produce any knots

For explanation I would say: The best WAY of representing this requirement is to draw the sequence in a circular form. The paired BASES are then joined by arcs. If the TOTAL STRUCTURE with all predicted base pairs is to be free of knots, none of the arcs must cross.

Correct option is (a) True

The EXPLANATION is: It is known that RNA functional motifs are structurally conserved. To maintain the secondary STRUCTURES while the homologous sequences evolve, a mutation OCCURRING in one position that is responsible for base PAIRING should be compensated for by a mutation in the corresponding base-pairing position so to maintain base pairing and the stability of the secondary structure.

The correct answer is (b) It uses the thermodynamic calculations only

The EXPLANATION is: It is a web-based program for RNA secondary STRUCTURE prediction. It combines dynamic programming and thermodynamic calculations for identifying themostable secondary structures with the lowest energy. It also produces DOT plots coupled with energy TERMS. This method is reliable for short sequences but becomes less accurate as the sequence length increases.

Correct answer is (a) True

To explain: For EXAMPLE, the PRODUCTION S1 → C S2 G could also be represented by 15 other base-pair combinations, and each of these has a CORRESPONDING probability. THUS, each production can be considered to be represented by a probability DISTRIBUTION over the possible outcomes.

Right option is (a) True

Explanation: As with hidden Markov models, the probability distribution of each PRODUCTION must be derived by training with known sequences. The ALGORITHMS used for training the SCFG and for aligning a sequence with the SCFG are somewhat DIFFERENT from those used with hidden Markov models, and the TIME and memory requirements are greater.

Correct option is (a) True

The EXPLANATION: One is BASED on the calculation of the MINIMUM free energy of the stable structure derived from a single RNA sequence. This can be considered an ab INITIO approach. The second is a comparative approach which infers structures based on an evolutionary comparison of multiple related RNA sequences.

Right choice is (b) interior loop

To elaborate: In ADDITION to the traditional secondary structural elements, base pairing between loops of different secondary structural elements can result in a higher LEVEL of structures such as pseudoknots, kissing hairpins, and hairpin–bulge contact. A pseudoknot loop refers to base pairing formed between loop RESIDUES within a hairpin loop and residues outside the hairpin loop.

The CORRECT option is (B) hairpin loop

Easy explanation: The bulge loop refers to a single STRANDED REGION connecting two adjacent base-paired segments so that it “bubbles” out in the middle of a double helix on ONE side. The multi-branch loop is also called helical junctions.

The correct OPTION is (a) partition function

For explanation I would SAY: This function HELPS to SELECT a number of suboptimal structures within a certain energy range. The MFOLD and RNAFold are two well-known programs USING the ab initio prediction method.

Correct CHOICE is (a) True

Explanation: Parameters for calculating different destabilizing energies have also been determined and can be used as penalties for secondary structure CALCULATIONS. This method WORKS by first finding all possible base-pairing patterns from a sequence and then calculating the TOTAL energy of a potential secondary structure by taking into account all the ADJACENT stabilizing and destabilizing forces.

Right answer is (b) False

For explanation: RNA is SINGLE STRANDED, ALTHOUGH an RNA molecule can self-hybridize at certain regions to form partial double-stranded structures. GENERALLY, mRNA is more or less LINEAR and non-structured, whereas rRNA and tRNA can only function by forming particular secondary and tertiary structures.

The correct answer is (a) True

The BEST explanation: The application of these GRAMMARS to sequence analysis has been extensively discussed elsewhere. The context-free GRAMMAR is suitable for finding groups of SYMBOLS in different parts of the input sequence that thus are not in the same context.

The correct choice is (b) False

Easiest explanation: The PROGRAM uses a combination of CLUSTAL and dynamic PROGRAMMING with a scoring scheme that includes covariation information to construct the alignment. A COMMONLY conserved structure for both sequences is subsequently DERIVED based on the alignment. To reduce computational complexity, the program ignores multi-branch loops and is only suitable for handling short RNA sequences.

Right answer is (b) False

To EXPLAIN: To evaluate all the different possible configurations and to find the most energetically favorable, several types of scoring matrices are used. The COMPLEMENTARY regions are EVALUATED by a DYNAMIC programming ALGORITHM to predict the most energetically stable molecule. The method is similar to the dynamic programming method used for sequence alignment.

Right answer is (a) G, U

For explanation I would SAY: There often exists non-canonical base pairing such as G and U base paring. The G–U base PAIR is less stable and normally OCCURS within a double-strand helix SURROUNDED by Watson–Crick base pairs. Finally, the tertiary structure is the three-dimensional arrangement of bases of the RNA molecule.

Right option is (a) True

For explanation: It was so DONE to evaluate parts of a new SCORING matrix in which the sequence is represented in two tandem copies on both the vertical and horizontal axes. The regions from i 1 to n and j 1 to n are used to calculate an energy V (i,j) for the best structure that includes an i, j BASE pair and is called the INCLUDED region.

Correct option is (b) are, will not be

The best explanation: The SELECTION of one SINGLE consensus structure is also a drawback because alternative and evolutionarily unconserved STRUCTURES are not predicted. The RNAalifold is an example of this TYPE of program based on predefined aligned sequences.

Correct answer is (a) Any LACK, deleterious

For explanation I would say: Based on this RULE, algorithms can be WRITTEN to search for the covariation patterns after a set of homologous RNA sequences are properly aligned. The detected correlated substitutions help to DETERMINE conserved base pairing in a SECONDARY structure.

Correct choice is (b) False

To elaborate: RNA secondary structure is composed primarily of double-stranded RNA regions FORMED by folding the single-stranded MOLECULE back on itself. To produce such double-stranded regions, a run of bases downstream in the RNA sequence must be complementary to another UPSTREAM run so that Watson–Crick base-pairing between the complementary nucleotides G/C and A/U (analogous to the G/C and A/T base pairs in DNA) can occur.

Correct answer is (a) multiple alternative structures, lowest energy

The EXPLANATION: The unique FEATURE of this program is that it does not require sequence similarity and therefore can HANDLE very divergent sequences. However, because of the computation complexity, the program only PREDICTS small RNA sequences such as tRNA with reasonable accuracy.