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101.

In comparative approach to RNA structure prediction, Dynalign is a ________ program.(a) Windows based(b) Fedora(c) UNIX(d) iOS based

Answer» Right option is (c) UNIX

The explanation is: Is a UNIX program with a free source code for downloading. Here, the user again provides two input sequences. The program calculates the possible secondary structures of each using a method similar to Mfold.
Discussion
102.

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.(a) multiple alternative structures, lowest energy(b) single structure, lowest energy(c) single structure, highest energy(d) multiple alternative structures, highest energy

Answer» 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.
Discussion
103.

____ wobble pairs may be produced in these double-stranded regions.(a) A/A(b) A/U(c) G/C(d) G/U

Answer» Right choice is (d) G/U

For explanation: As in DNA, the G/C base pairs contribute the greatest energetic stability to the molecule, with A/U base pairs contributing less stability than G/C, and G/U wobble base pairs contributing the least. From the RNA structures that have been solved, these base pairs and a number of additional ones have been identified.
Discussion
104.

Which of the following is not among the methods for finding localized sequence similarity?(a) Profile Analysis(b) Block Analysis(c) Extraction of Blocks from a Global or Local MSA(d) Pattern blocking

Answer» The correct option is (d) Pattern blocking

For explanation I would say: Pattern Searching is the correct name of the method for finding localized sequence similarity. This type of analysis was performed on groups of related proteins, and the amino acid patterns that were located may be found in the Prosite catalog.
Discussion
105.

Two considerations arise in trying to tune the PSSM so that it adequately represents the training sequences. Which of the following is not their description?(a) If a given column in 20 sequences has only isoleucine, it is not very likely that different amino acid will be found in other sequences with that motif because the residue is probably important for function(b) If a given column in 20 sequences has only isoleucine, it is very likely that different amino acid will be found in other sequences with that motif because the residue is probably important for function(c) If the number of sequences with the found motif is large and reasonably diverse, the sequences represent a good statistical sampling of all sequences that are ever likely to be found with that same motif(d) Another column in the motif from the 20 sequences may have several amino acids, and some amino acids may not be represented at all

Answer» Right option is (b) If a given column in 20 sequences has only isoleucine, it is very likely that different amino acid will be found in other sequences with that motif because the residue is probably important for function

Easy explanation: The PSSM is constructed by a simple logarithmic transformation of a matrix giving the frequency of each amino acid in the motif. Even more variation may be expected at that position in other sequences, although the more abundant amino acids already found in that column would probably be favored.
Discussion
106.

Which of the following is not a benefit of BLAST?(a) Handling of gaps(b) Speed(c) More sensitive(d) Statistical rigor

Answer» The correct choice is (a) Handling of gaps

For explanation: In addition to this, user friendly UI of BLAST is also one of its benefits. However, it does not handle gaps well. In that case gapped BLAST is better.
Discussion
107.

Which of the following is an incorrect statement?(a) WebMol is a web-based program built based on a modified RasMol code and thus shares many similarities with RasMol(b) WebMol is a web-based program that is totally different from RasMol(c) Chime is a plug-in for web browsers(d) Chime is not a standalone program and has to be invoked in a web browser

Answer» Right choice is (b) WebMol is a web-based program that is totally different from RasMol

Easy explanation: Chime is also derived from RasMol and allows interactive display of graphics of protein structures inside a web browser. RasMol runs directly on a browser of any type as an applet and is able to display simple line drawing models of protein structures. It also has a feature of interactively displaying Ramachandran plots for structure model evaluation.
Discussion
108.

Members within the ____ fold ______ have evolutionary relationships.(a) same, always(b) same, do not always(c) one, always(d) different, do not

Answer» Right choice is (b) same, do not always

Easy explanation: Folds consist of superfamilies with a common core structure, which is determined manually. This level describes similar overall secondary structures with similar orientation and connectivity between them. Members within the same fold do not always have evolutionary relationships. Some of the shared core structure may be a result of analogy. Classes consist of folds with similar core structures.
Discussion
109.

Which of the following is not correct about the α-Helices?(a) An α-helix has a main chain backbone conformation that resembles a corkscrew(b) Nearly all known α-helices are right handed, exhibiting a leftward spiral form(c) Nearly all known α-helices are right handed, exhibiting a rightward spiral form(d) In right handed helix, there are 3.6 amino acids per helical turn

Answer» Correct choice is (b) Nearly all known α-helices are right handed, exhibiting a leftward spiral form

Easiest explanation: The structure is stabilized by hydrogen bonds formed between the main chain atoms of residues i and i + 4. The hydrogen bonds are nearly parallel with the helical axis. The average φ and ψ angles are 60◦ and 45◦, respectively, and are distributed in a narrowly defined region in the lower left region of a Ramachandran plot.
Discussion
110.

Which of the following is incorrect about Multiple Structure Alignment?(a) The alignment strategy is different than the Clustal sequence alignment using a progressive approach(b) All structures are first compared in a pairwise fashion(c) A distance matrix is developed based on structure similarity scores such as RMSD(d) The aligned structures create a median structure that allows other structures to be progressively added for comparison based on the hierarchy described in the guide tree

Answer» Right answer is (a) The alignment strategy is different than the Clustal sequence alignment using a progressive approach

Explanation: In addition to pairwise alignment, a number of algorithms can also perform multiple structure alignment. The alignment strategy is similar to the Clustal sequence alignment using a progressive approach. When all the structures in the set are added, this eventually creates a multiple structure alignment.
Discussion
111.

Which of the following is untrue about Expectation Maximization (EM) method?(a) It is used to find hidden motifs(b) The method works by first making a random or guessed alignment of the sequences to generate a trial PSSM(c) The trial PSSM is used to compare with each sequence individually(d) The log odds scores of the PSSM are modified at the end of the process

Answer» Correct option is (d) The log odds scores of the PSSM are modified at the end of the process

The explanation is: The log odds scores of the PSSM are modified in each iteration to maximize the alignment of the matrix to each sequence. During the iterations, the sequence pattern for the conserved motifs is gradually “recruited” to the PSSM.
Discussion
112.

A gap opening penalty for any gap (g) and a gap extension penalty for each element in the gap (r) are most often used, to give a total gap score wx, according to the equation ______(a) wx – rx = -g(b) wx = g – rx(c) wx = g + rx(d) wx + g + rx = 0

Answer» Right answer is (c) wx = g + rx

For explanation I would say: wx = g + rx is the equation where x is the length of the gap. in some formulations of the gap penalty, the equation wx  = g  + r (x – 1) is used. Thus, the gap extension penalty is not added to the gap opening penalty until the gap size is 2.
Discussion
113.

Which of the following is untrue regarding the gap penalty used in dynamic programming?(a) Gap penalty is subtracted for each gap that has been introduced(b) Gap penalty is added for each gap that has been introduced(c) The gap score defines a penalty given to alignment when we have insertion or deletion(d) Gap open and gap extension has been introduced when there are continuous gaps (five or more)

Answer» The correct option is (b) Gap penalty is added for each gap that has been introduced

Best explanation: Dynamic programming algorithms use gap penalties to maximize the biological meaning. The open penalty is always applied at the start of the gap, and then the other gaps following it is given with a gap extension penalty which will be less compared to the open penalty. Typical values are –12 for gap opening, and –4 for gap extension.
Discussion
114.

Which of the following is incorrect?(a) Smith–Waterman algorithm is the fastest(b) Smith–Waterman algorithm is comparatively slower method(c) To speedup up comparison, heuristic methods are used(d) Heuristic algorithms perform faster searches

Answer» The correct choice is (a) Smith–Waterman algorithm is the fastest

For explanation: Searching a large database using the dynamic programming methods, such as the Smith–Waterman algorithm, although accurate and reliable, is too slow and impractical when computational resources are limited. To speed up the comparison, heuristic methods have to be used. The heuristic algorithms perform faster searches because they examine only a fraction of the possible alignments examined in regular dynamic programming.
Discussion
115.

In Smith–Waterman algorithm, in initialization Step, the _________ row and ________ column are subject to gap penalty.(a) first, first(b) first, second(c) second, First(d) first, last

Answer» The correct answer is (a) first, first

The explanation: In Smith–Waterman algorithm, first row and first column are set to 0. In the Needleman Wunsch algorithm, First row and first column are subject to gap penalty.
Discussion
116.

When random or unrelated sequences are compared using a global alignment method, they can have ____________ reflecting the tendency of the global algorithm to match as many characters as possible.(a) very low scores(b) very high scores(c) moderate scores(d) low scores

Answer» The correct choice is (b) very high scores

Easiest explanation: The significance of the scores of global alignments, is more difficult to determine. Using the Needleman-Wunsch algorithm and a suitable scoring system, there are many ways to produce a global alignment between any pair of sequences, and the scores of many different alignments may be quite similar hence the scores obtained might be unusually high.
Discussion