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Multiple choice question for engineering

Set 1

1. Which of the following is correct regarding gantry girders?
a) It is laterally supported except at the columns
b) It is subjected to impact load
c) It should not be analysed for unsymmetrical bending
d) It is not subjected to longitudinal load

View Answer

Answer: b [Reason:] Gantry girder are different from beams in buildings. It is generally laterally unsupported except at the columns. It is subjected to impact load. It must be analysed for unsymmetrical bending because of lateral thrust from the starting and stopping of the crab. It is subjected to longitudinal load due to starting and stopping of crane bridge itself. They are always simply supported.

2. Which of the following loads are not considered in the design of gantry girders?
a) longitudinal loads
b) gravity loads
c) lateral loads
d) wind loads

View Answer

Answer: d [Reason:] The loads considered in the design of gantry girders are vertical loads or gravity loads, longitudinal loads, lateral loads and impact loads. The vertical force is the reaction from crane girder, acting vertically downward. The longitudinal thrust is due to starting and stopping of crane acting in longitudinal direction. The lateral thrust is due to starting and stopping of the crab acting horizontally normal to the gantry girder.

3. The wheel load transferred from trolley to gantry girder is given by
a) W1 = [Wt(Lc+L1)]/(2Lc)
b) W1 = [Wt(Lc-L1)](2Lc)
c) W1 = [Wt(Lc-L1)]/(2Lc)
d) W1 = [Wt(Lc+L1)]/( Lc)

View Answer

Answer: c [Reason:] Since trolley moves on the crane girder along the span of truss, its weight is transferred to the crane wheels as the axle load and finally to gantry girder. The wheel load transferred from trolley to gantry girder is given by W1 = [Wt(Lc-L1)]/(2Lc), where W1 is load of each wheel on gantry girder, Wt is weight of trolley or crab car, Lc is distance between gantry giders, L1 is distance between centre of gravity of trolley and gantry.

4. For gantry girders carrying electrically operated overhead travelling cranes, the lateral forces are increased by ____ for impact allowance.
a) 10% of weight of crab and weight lifted on the crane
b) 20% of weight of crab and weight lifted on the crane
c) 25% of maximum static wheel load
d) 50% of maximum static wheel load

View Answer

Answer: a [Reason:] For gantry girders carrying electrically operated overhead travelling cranes, the lateral forces are increased by 10% of weight of crab for impact allowance and weight lifted on the crane. The vertical forces can be increased by 25% of maximum static wheel load.

5. For gantry girders carrying hand operated cranes, the vertical forces are increased by____ for impact allowance
a) 10% of maximum static wheel load
b) 25% of maximum static wheel load
c) 10% of weight of crab and weight lifted on the crane
d) 20% of weight of crab and weight lifted on the crane

View Answer

Answer: c [Reason:] For gantry girders carrying hand operated cranes, the vertical forces are increased by 10% of maximum static wheel load for impact allowance. The lateral forces can be increased by 5% of weight of crab and weight lifted on the crane.

6. Fatigue effect for light and medium duty cranes need not be checked if
a) Nsc > 10×106 [(27/γmft)/γmt].
b) Nsc < 5×106 [(27/γmft)/γmt]3
c) Nsc > 5×106 [(27/γmft)/γmt]2
d) Nsc < 5×106 [(27/γmftmt].

View Answer

Answer: b [Reason:] Fatigue effect for light and medium duty cranes need not be checked if normal and shear design stress ranges f ≤ (27/γmft) or if actual number of stress cycles, Nsc < 5×106 [(27/γmft)/γmt]3, where f = actual fatigue stress range, γmft = partial safety factor for strength, γmf = partial safety factor for material = 1.10.

7. The maximum wheel load is obtained when
a) crane crab is farthest to gantry girder
b) crane crab is closest to gantry girder
c) crane crab is not attached
d) crane crab is at mid span

View Answer

Answer: b [Reason:] The maximum wheel load is obtained when crane crab is closest to gantry girder. The crab in such position on the crane girder gives maximum reaction on the gantry girder. The vertical reaction of crane girder is transferred through its two wheels on to the gantry girder. Therefore, the maximum wheel load is half of this reaction. This maximum wheel load is then increased for impact and used for design of gantry girder.

8. The bending moment due to dead load of girder is maximum at
a) one-third distance at span
b) two-third distance at span
c) end of span
d) centre of span

View Answer

Answer: d [Reason:] The bending moment considered in the design of gantry girder are the bending moment due to maximum wheel loads (with impact) and the bending moment due to dead load of the girder and rails. The bending moment due to dead loads is maximum at the centre of span.

9. What is the maximum vertical deflection allowed for a gantry girder where the cranes are manually operated?
a) L/500
b) L/700
c) L/600
d) L/800

View Answer

Answer: a [Reason:] The vertical deflection of gantry girder where the cranes are manually operated should not exceed L/500, where L is the span of gantry girder. The maximum vertical deflection allowed for a gantry girder where the cranes are travelling overhead and operated electrically upto 500kN is L/750 and operated electrically over 500kN is L/1000. When gantry girders carry moving loads such as charging cars, the deflection should not exceed L/600.

10. The minimum recommended rise of trusses with Galvanised Iron sheets is
a) 1 in 12
b) 1 in 6
c) 1 in 10
d) 1 in 18

View Answer

Answer: b [Reason:] The pitch of truss depends upon the roofing material. The minimum recommended rise of trusses with galvanised iron sheets is 1 in 6 and with asbestos cement sheets is 1 in 12.

11. The economic spacing of roof truss depends on
a) cost of purlins only
b) cost of purlins and cost of roof covering
c) dead loads
d) cost of roof covering and dead loads

View Answer

Answer: b [Reason:] The economic spacing of the truss is the spacing that makes the overall cost of trusses, purlins, roof coverings, columns, etc. the minimum. It depends upon the relative cost of trusses, purlins, roof coverings, spacing of columns, etc. If the spacing is large, the cost of these trusses per unit area decreases but the cost of purlin increases. But if the spacing of trusses is small, the cost of trusses per unit area increases. Roof coverings cost more if the spacing of trusses is large.

12. Which of the following is true for economic spacing?
a) cost of trusses should be equal to twice the cost of purlins
b) cost of trusses should be equal to twice the cost of purlins minus cost of roof coverings
c) cost of trusses should be equal to the cost of purlins plus cost of roof coverings
d) cost of trusses should be equal to twice the cost of purlins plus cost of roof coverings

View Answer

Answer: d [Reason:] For economic spacing of roof trusses, the cost of trusses should be equal to twice the cost of purlins plus cost of roof coverings. This equation is used for checking the spacing of trusses and not for design of trusses.

13. Which of the following load combination is not considered for design of roof trusses?
a) Dead load + crane load
b) Dead load + wind load
c) Dead load + earthquake load
d) Dead load + live load + wind load

View Answer

Answer: c [Reason:] Earthquake loads are not significant for roof trusses because of the small self weights. The following load combinations can be considered : (i) Dead load + snow load, (ii) Dead load + partial/full live load, (iii) dead load + live load + internal positive air pressure, (iv) dead load + live load + internal suction air pressure, (v) dead load + live load + wind load.

14. Live load for roof truss should not be less than
a) 0.4kN/m2
b) 0.2kN/m2
c) 0.75kN/m2
d) 0.8kN/m2

View Answer

Answer: a [Reason:] The live load for roof truss should not be less than 0.4kN/m2. For roof slopes ≤ 10o and access provided, the live load to be taken is 1.5kN/m2 of plan area. For roof slopes > 10o and access is not provided , the live load to be taken is 0.75kN/m2 of plan area.

Set 2

1. A plate girder is used when
a) span is large and loads are heavy
b) span is small and loads are heavy
c) span is small and loads are light
d) span is large and loads are light

View Answer

Answer: a [Reason:] A plate girder is deep flexural member used to carry loads that cannot be economically carried by rolled beams. When load is heavier and span is also large, there are three options : i) two or more I0sections, connected appropriately (ii) plate girder (iii)truss girder. Of the above alternatives, first is uneconomical. So, plate girder or truss girder can be used. Plate girder is used since cost of fabrication of truss girder is high.

2. Why plate girder is preferred over truss girder?
a) plate girder requires costly maintenance
b) higher vertical clearance required for plate girder than truss girder
c) cost of fabrication of plate girder is high
d) cost of fabrication of truss girder is high

View Answer

Answer: d [Reason:] When load is heavier and span is also large, either plate girder or truss girder can be used. But, plate girder is preferred because of the disadvantages of truss girder. The disadvantages of truss girder are higher cost of fabrication and erection, problem of vibration and impact, requirements of higher vertical clearance and costly maintenance.

3. Bending resistance of plate girders can be increased by
a) decreasing distance between flanges
b) increasing distance between flanges
c) reducing distance between flanges to half
d) bending resistance cannot be increased

View Answer

Answer: b [Reason:] Plate girders are built-up flexural members. Their bending resistance can be increased by increasing the distance between flanges. This also increases the shear resistance as web area increases.

4. Which of the following is economical if depth is limited and loads are too large?
a) rolled section beam
b) truss girder
c) welded box plate girder
d) bolted box plate girder

View Answer

Answer: c [Reason:] When the loads and span are large, plate girder sections either with riveted/bolted connections or welded connections may be provided. The number of flange plates can be increased depending upon the moment to be resisted. If depth is limited and loads are too large, welded box plate girder is provided. A box girder with riveted/bolted connections can b e provided but it is too costly as compared to welded one. Box girders have great resistance to lateral buckling.

5. An ideal bolted plate girder section consists of
a) flange angles and cover plates for both compression flange and tension flange
b) flange angles and cover plates for compression flange and only flange angle for tension flange
c) only flange angle for compression flange and flange angles and cover plates for tension flange
d) flange angles for both compression flange and tension flange

View Answer

Answer: b [Reason:] An ideal bolted plate girder section consists of flange angles and cover plates for compression flange and only flange angle for tension flange. The various elements of riveted/bolted/welded plate girder are : web plate, flange angles with or without cover plates for riveted/bolted plate girder and only flange angles for welded plate girder, stiffeners – bearing, transverse and longitudinal, splices for web and flange.

6. The modes of failure of plate girder are
a) by yielding of compression flange only
b) by buckling of tension flange only
c) by yielding of tension flange and buckling of compression flange
d) by yielding of compression flange and buckling of tension flange

View Answer

Answer: c [Reason:] The limit states considered for plate girder are yielding of tension flange and buckling of compression flange. The compression flange buckling can take place in various ways, such as vertical buckling into the web or flange local buckling. Flange buckling can also be caused due to lateral-torsional buckling.

7. At high shear locations in the girder web, principal plane will be ______ to longitudinal axis of member
a) inclined
b) parallel
c) perpendicular
d) coincides

View Answer

Answer: a [Reason:] At high shear locations in the girder web, usually near supports and neutral axis, the principal planes will be inclined to longitudinal axis of the member. The principal stresses will be diagonal tension and diagonal compression along the principal planes.

8. Which of the following causes web buckling in plate girder?
a) diagonal tension
b) diagonal compression
c) diagonal tension and diagonal compression
d) neither diagonal tension nor diagonal compression

View Answer

Answer: b [Reason:] The principal planes will be inclined to longitudinal axis of the member at high shear locations in the girder web. Along the principal planes, the principal stresses will be diagonal tension and diagonal compression. Diagonal tension does not cause any problem but diagonal compression causes the web to buckle in the direction perpendicular to its action.

9. Which of the following statement is correct for reducing web buckling due to diagonal compression?
a) not providing web stiffeners to increase shear strength
b) providing web stiffeners to reduce shear strength
c) increasing depth-to-thickness ratio
d) reducing depth-to-thickness ratio

View Answer

Answer: d [Reason:] Diagonal compression causes web to buckle in the direction perpendicular to its action. This problem can be solved by any of the following ways : (i) reduce depth-to-thickness ratio of web such that problem is eliminated, (ii) provide web stiffeners to form panels that would enhance shear strength of web, (iii) provide web stiffeners to form panels that would develop tension field action to resist diagonal compression.

10. Which of the following is correct during tension field action?
a) web can resist diagonal compression
b) horizontal component of diagonal compression is supported by flanges
c) vertical component of diagonal compression is supported by flanges
d) vertical component of diagonal compression is supported by stiffeners

View Answer

Answer: b [Reason:] As web begins to buckle , the web loses its ability to resist diagonal compression. The diagonal compression is transferred to transverse stiffeners and flanges. The vertical component of diagonal compression is supported by stiffeners and horizontal component is resisted by flanges. The web resists only diagonal tension and this behaviour of web is called tension field action.

11. Which of the statement is not true about intermediate stiffeners?
a) they reduce shear capacity of web
b) they improve shear capacity of web
c) they can be used to develop tension field action
d) their main purpose is to provide stiffness to the web

View Answer

Answer: a [Reason:] Intermediate stiffeners can be used to develop tension field action and improve shear capacity of web. The main purpose of these stiffeners is to provide stiffness to the web rather than to resist the applied loads. Additional stiffeners called bearing stiffeners are provided at points of concentrated loads to protect the web from the direct compressive loads.

Set 3

1. The eukaryotic transcription initiation is less dependent on transcription factors.
a) True
b) False

View Answer

Answer: b [Reason:] The eukaryotic transcription initiation requires cooperation of a large number of transcription factors. Co-operativity means that the promoter regions tend to contain a high density of protein-binding sites. Thus, finding a cluster of transcription factor binding sites often enhances the probability of individual binding site prediction.

2. CpGProD is a web-based program that predicts promoters containing a high density of CpG islands_______
a) in archea genomic sequences
b) in mammalian genomic sequences
c) in eukaryotic and bacterial genomic sequences
d) only in bacterial genomic sequences

View Answer

Answer: b [Reason:] It calculates moving averages of GC% and CpG ratios (observed/expected) over a window of a certain size (usually 200 bp). When the values are above a certain threshold, the region is identified as a CpG island.

3. Which of the following is incorrect regarding Eponine?
a) It is a web-based program that predicts transcription start sites
b) It is a web-based program that particularly predicts tranpososons and retropososons
c) The regulatory sites include the TATA box, the CCAAT box, and CpG islands
d) It is based on a series of pre-constructed PSSMs of several regulatory sites

View Answer

Answer: b [Reason:] The query sequence from a mammalian source is scanned through the PSSMs. The sequence stretches with high-score matching to all the PSSMs, as well as matching of the spacing between the elements, are declared transcription start sites. A Bayesian method is also used in decision making.

4. Which of the following is incorrect regarding Cluster-Buster?
a) It is an HMM-based web-based program
b) A query sequence is scanned with a window size of 1 kb for putative regulatory motifs using motif HMMs
c) It works by detecting a region of high concentration of unknown transcription factor binding sites and regulatory motifs at the initiation
d) It is designed to find clusters of regulatory binding sites

View Answer

Answer: c [Reason:] It works by detecting a region of high concentration of known transcription factor binding sites and regulatory motifs. If multiple motifs are detected within a window, a positive score is assigned to each motif found. The total score of the window is the sum of each motif score subtracting a gap penalty, which is proportional to the distances between motifs. If the score of a certain region is above a certain threshold, it is predicted to contain a regulatory cluster.

5. Which of the following is incorrect regarding First EF?
a) It is a program that predicts promoters for bacterial DNA
b) It is a web-based program that predicts promoters for human DNA
c) It stands for First Exon Finder
d) It integrates gene prediction with promoter prediction

View Answer

Answer: a [Reason:] It uses quadratic discriminant functions (see Chapter 8) to calculate the probabilities of the first exon of a gene and its boundary sites. A segment of DNA (15 kb) upstream of the first exon is subsequently extracted for promoter prediction on the basis of scores for CpG islands.

6. McPromoter, a web-based program, uses a neural network to make promoter predictions.
a) True
b) False

View Answer

Answer: a [Reason:] It has a unique promoter model containing six scoring segments. The program scans a window of 300 bases for the likelihoods of being in each of the coding, noncoding, and promoter regions.

7. The input for the neural network includes parameters for sequence physical properties, such as ______
a) DNA bendability
b) Signals such as the TATA box
c) Signals such as initiator box
d) Signals such as CpAA islands

View Answer

Answer: d [Reason:] As seen, the correct answer is CpG in option d. The hidden layer combines all the features to derive an overall likelihood for a site being a promoter. Another unique feature is that McPromoter does not require that certain patterns must be present, but instead the combination of all features is important. For instance, even if the TATA box score is very low, a promoter prediction can still be made if the other features score highly. The program is currently trained for Drosophila and human sequences.

8. TSSW is a web program that distinguishes promoter sequences from non-promoter sequences based on a combination of unique content information such as hexamer/trimer frequencies and signal information such the TATA box in the promoter region.
a) True
b) False

View Answer

Answer: a [Reason:] As mentioned here, TSSW uses unique content information such as hexamer/trimer frequencies and signal information such the TATA box in the promoter region. The values are fed to a linear discriminant function to separate true motifs from background noise.

9. Which of the following is incorrect regarding CONPRO?
a) It is a web-based program that uses a consensus method
b) It is used to identify promoter elements for human DNA
c) cDNA does not play a role in prediction
d) The program uses the information to search the human genome database for the position of the gene

View Answer

Answer: c [Reason:] To use the program, a user supplies the transcript sequence of a gene (cDNA). It then uses the GENSCAN program to predict 5’ untranslated exons in the upstream region. Once the 5’-most exon is located, a further upstream region (1.5 kb) is used for promoter prediction, which relies on a combination of five promoter prediction programs, TSSG, TSSW, NNPP, PROSCAN, and PromFD.

10. In CONPRO, for each program, the highest score prediction is taken as the promoter in the region.
a) True
b) False

View Answer

Answer: a [Reason:] If three predictions fall within a 100-bp region, this is considered a consensus prediction If no three-way consensus is achieved, TSSG and PromFD predictions are taken. Because no coding sequence is used in prediction, specificity is improved relative to each individual program.

Set 4

1. On analysis of the alignment scores of random sequences will reveal that the scores follow a different distribution than the normal distribution called the _________
a) Gumbel equal value distribution
b) Gumbel extreme value distribution
c) Gumbel end value distribution
d) Gumbel distribution

View Answer

Answer: b [Reason:] Originally, the significance of sequence alignment scores was evaluated on the basis of the assumption that alignment scores followed a normal statistical distribution. If sequences are randomly generated in a computer by a Monte Carlo or sequence shuffling method, as in generating a sequence by picking marbles representing four bases or 20 amino acids out of a bag, the distribution may look normal at first glance. But on further analysis the above result was obtained.

2. The statistical analysis of alignment scores is much better understood for ________ than for _______
a) global alignments, local alignments
b) local alignments, global alignments
c) global alignments, any other alignment method
d) Needleman-Wunsch alignment, Smith-Waterman alignment

View Answer

Answer: b [Reason:] Smith-Waterman alignment algorithm and the scoring system used to produce a local alignment are designed to reveal regions of closely matching sequence with a positive alignment score. In random or unrelated sequence alignments, these regions are rarely found. Hence, their presence in real sequence alignments is significant, and the probability of their occurring by chance alignment of unrelated sequences can be readily calculated.

3. 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

View Answer

Answer: b [Reason:] 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.

4. Which of the following are not related to Needleman-Wunsch alignment algorithm?
a) Global alignment programs use this algorithm
b) The output is a positive number
c) Small changes in the scoring system can produce a different alignment
d) Changes in the scoring system can produce the same alignment

View Answer

Answer: d [Reason:] In general, global alignment programs use the Needleman-Wunsch alignment algorithm and a scoring system that scores the average match of an aligned nucleotide or amino acid pair as a positive number. Hence, the score of the alignment of random or unrelated sequences grows proportionally to the length of the sequences. In addition, there are many possible different global alignments depending on the scoring system chosen, and small changes in the scoring system can produce a different alignment.

5. Waterman, in1989, provided a set of means and standard deviations of global alignment scores between random DNA sequences, using mismatch and gap penalties that produce a linear increase in score with _______ a distinguishing feature of global alignments.
a) alignment score
b) sequence score
c) sequence length
d) scoring system

View Answer

Answer: c [Reason:] In the algorithm provided by Waterman, the score of the alignment of random or unrelated sequences grows proportionally to the length of the sequences. However, these values are of limited use because they are based on a simple gap scoring system.

6. Who suggested that the global alignment scores between unrelated protein sequences followed the extreme value distribution, similar to local alignment scores? And when?
a) Abagyan and Batalov, in 1981
b) Chvátal and Lipman, in 1984
c) Abagyan and Batalov, in 1997
d) Chvátal and Sankoff, in 1995

View Answer

Answer: c [Reason:] Abagyan and Batalov, in 1997, suggested the above observation. However, since the scoring system that they used favored local alignments, these alignments they produced may not be global but local. Unfortunately, there is no equivalent theory on which to base an analysis of global alignment scores as there is for local alignment scores.

7. _______ analyzed the distribution of scores among 100 vertebrate nucleic acid sequences and compared these scores with randomized sequences prepared in different ways.
a) Lipman, in 1984
b) Batalov, in 1964
c) Waterman, in 1987
d) Lipman, in 1967

View Answer

Answer: a [Reason:] When the randomized sequences were prepared by shuffling the sequence to conserve base composition, as was done by Dayhoff and others, the standard deviation was approximately one-third less than the distribution of scores of the natural sequences. Thus, natural sequences are more variable than randomized ones, and using such randomized sequences for a significance test may lead to an overestimation of the significance.

8. If the random sequences were prepared in a way that maintained the local base composition by producing them from overlapping fragments of sequence, the distribution of scores has a_______ standard deviation that is closer to the distribution of the natural sequences.
a) lowest
b) higher
c) lower
d) moderate

View Answer

Answer: c [Reason:] The conclusion from the above is that the presence of conserved local patterns can influence the score in statistical tests such that an alignment can appear to be more significant than it actually is. Although this study was done using the Smith-Waterman algorithm with nucleic acids, the same cautionary note applies for other types of alignments.

9. The GCG alignment programs have a RANDOMIZATION option, which shuffles the second sequence and calculates similarity scores between the unshuffled sequence and each of the shuffled copies.
a) True
b) False

View Answer

Answer: a [Reason:] If the new similarity scores are significantly smaller than the real alignment score, the alignment is considered significant. This analysis is only useful for providing a rough approximation of the significance of an alignment score and can easily be misleading.

10. Dayhoff, 1978- 1983, devised a second method for testing the relatedness of two protein sequences that can accommodate some local variation. Where this method is useful?
a) For finding repeated regions within a sequence
b) For finding similar regions that are in a different order in two sequences
c) For finding small conserved region such as an active site
d) For finding huge regions within sequences

View Answer

Answer: d [Reason:] As used in a computer program called RELATE (Dayhoff 1978), all possible segments of a given length of one sequence are compared with all segments of the same length from another. An alignment score using a scoring matrix is obtained for each comparison to give a score distribution among all of the segments. A segment comparison score in standard deviation units is calculated as the difference between the values for real sequences minus the average value for random sequences divided by the standard deviation of the scores from the random sequences.

Set 5

1. For what type of sequences Gibbs sampling is used?
a) Closely related sequences
b) Distinctly related sequences
c) Distinctly related sequences that share common motifs
d) Closely related sequences that share common motifs

View Answer

Answer: c [Reason:] Often, distantly related sequences that share common motifs cannot be readily aligned. For example, the sequences for the helix-turn-helix motif in transcription factors can be subtly different enough that traditional multiple sequence alignment approaches fail to generate a satisfactory answer. For detecting such subtle motifs, more sophisticated algorithms such as expectation maximization (EM) and Gibbs sampling are used.

2. 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

View Answer

Answer: d [Reason:] 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.

3. Which of the following is true about Expectation Maximization (EM) method?
a) The log odds scores of the PSSM are modified at the end of the process
b) The procedure stops prematurely if the scores reach convergence
c) The final result is not sensitive to the initial alignment
d) Local optimum is an advantage of EM method

View Answer

Answer: b [Reason:] The final result is sensitive to the initial alignment. The Local optimum is actually a drawback of EM method. It is same as the fact that the procedure stops prematurely if the scores reach convergence.

4. MEME stands for _____________
a) Multiple Expectation Maximization for Motif Elicitation
b) Multiple Expectation Maximization for Motif Extraction
c) Mega Expectation Maximization for Motif Elicitation
d) Micro Expectation Maximization for Motif Extraction

View Answer

Answer: a [Reason:] Multiple Expectation Maximization for Motif Elicitation is a web-based program that uses the EM algorithm to find motifs either for DNA or protein sequences. It uses amodified EM algorithm to avoid the local minimum problem.

5. In the web-based program MEME, the computation is a _____ step procedure.
a) one
b) two
c) three
d) four

View Answer

Answer: b [Reason:] In constructing a probability matrix, it allows multiple starting alignments and does not assume that there are motifs in every sequence. Also, the computation is a two-step procedure which includes generation of sequence motif and finding highest score.

6. Gibbs is a web-based program that uses the Gibbs sampling approach to look for _____ gap-free segments for either DNA or protein sequences.
a) short, partially conserved
b) long, partially conserved
c) long, conserved
d) short, not conserved

View Answer

Answer: a [Reason:] Gibbs sampling approach to look for short, partially conserved gap-free segments for either DNA or protein sequences. To ensure accuracy, more than twenty sequences of the exact same length should be used.

7. A multiple sequence alignment or a motif is often represented by a graphic representation
called a ______
a) logo
b) motto
c) algorithm
d) algo

View Answer

Answer: a [Reason:] In a logo, each position consists of stacked letters representing the residues appearing in a particular column of a multiple alignment. This graphic representation called a logo.

8. The overall height of a logo position reflects how conserved the position is, and the _____ of each letter in a position reflects the _______ of the residue in the alignment.
a) height, relative frequency
b) width, relative frequency
c) height, amplitude
d) width, amplitude

View Answer

Answer: a [Reason:] The height expresses the data about the extent of the conservation of the position and each letter shows the frequency of that particular residue. The amplitude, here in this case, is irrelevant option.

9. Conserved positions have _____ residues and bigger symbols.
a) fewer
b) more
c) maximum
d) minimum

View Answer

Answer: a [Reason:] The options maximum and minimum are comparatively obsolete as there involves the studies of alignment. Conserved positions have fewer residues and bigger symbols; whereas less conserved positions have a more heterogeneous mixture of smaller symbols stacked together. In general, a sequence logo provides a clearer description of a consensus sequence.

10. _______ is an interactive program for generating sequence logos.
a) EMBOSS
b) WebLogo
c) LOGOLY
d) BLAST

View Answer

Answer: b [Reason:] In WebLogo, a user needs to enter the sequence alignment in FASTA format to allow the program to compute the logos. A graphic file is returned to the user as a result.