Multiple choice question for engineering
1. Which of the given statements is incorrect about global gene regulation?
a) One way to obtain useful information about a genome is to determine which genes are induced or repressed in response to a phase of the cell cycle
b) Sets of a gene whose expression rises and falls under the same condition are likely to have a related function
c) Sets of a gene whose expression rises and falls under the same condition are likely to have dissimilar functions
d) Cell cycle is a developmental phase, or a response to the environment
2. Which of the given statements is incorrect about Microarray (or microchip) analysis?
a) It is a new technology in which all of the genes of an organism are represented by oligonucleotide sequences spread out in an 80 x 80 array on microscope slides
b) The oligonucleotide sequences cannot be synthesized directly on the slide
c) The oligonucleotides are collectively hybridized to a labeled cDNA library prepared by reverse-transcribing mRNA from cells
d) The amount of label binding to each oligonucleotide spot reflects the amount of mRNA in the cell
3. Once a set of genes that are co-regulated has been found, the promoter regions of these genes may be analyzed for conserved patterns that represent sites of interaction with specific transcription factors.
4. Which of the given statements is incorrect about Microarray Analysis?
a) It is designed to detect global changes in transcription in a genome
b) It provides information about the levels of protein products of the genes
c) The proteins are first separated in a column on the basis of size and then across a second dimension on a slab on the basis of charge
d) Labeled protein samples may also be extracted from treated cells and separated by two-dimensional gel electrophoresis
5. In cluster analysis of microarray data– If Xi is the log odds value for gene X at time i, then for two genes X and Y and N observations, a similarity score is calculated. S(X,Y) is also known as the Pearson correlation coefficent. Xoffset and Yoffset can be the mean of the observations on X or Y, respectively, in which case is the standard deviation, or else Xoffset and Yoffset can be set to zero when a reference state is used.Which of the following best represents it?
6. In cluster analysis of microarray data– A node is created between the _____ scoring pair, and the gene expressed profiles of these two genes are averaged and the joined elements are weighted by the _____ of elements they contain.
a) lowest, frequency
b) average, sequence
c) lowest, number
d) highest, number
7. In cluster analysis of microarray data– For n genes, the process is repeated ____ times until a single element remains.
8. The hierarchical clustering method generates a similarity score [S(X,Y)] for all gene combinations, places the scores in a matrix, joins those genes that have the highest score, and then continues to join progressively less similar pairs.
9. In Self-organizing maps a choice is made of a number of clusters by which to organize the data.
10. SVMs (Support vector machines) are a binary classification method to discriminate one set of data points from another
11. In SVMs (Support vector machines) Data points are log-transformed and normalized as in method A, where for N observations of a gene i, the log transform Xi of the expression level Ei and reference level Ri is _____
1. When did Needleman-Wunsch first describe the algorithm for global alignment?
2. Which of the following does not describe dynamic programming?
a) The approach compares every pair of characters in the two sequences and generates an alignment, which is the best or optimal
b) Global alignment algorithm is based on this method
c) Local alignment algorithm is based on this method
d) The method can be useful in aligning protein sequences to protein sequences only
3. Which of the following is not an advantage of Needleman-Wunsch algorithm?
a) New algorithmic improvements as well as increasing computer capacity make possible to align a query sequence against a large DB in a few minutes
b) Similar sequence region is of same order and orientation
c) This does not help in determining evolutionary relationship
d) If you have 2 genes that are already understood as closely related, then this type of algorithm can be used to understand them in further details
4. Which of the following is not a disadvantage of Needleman-Wunsch algorithm?
a) This method is comparatively slow
b) There is a need of intensive memory
c) This cannot be applied on genome sized sequences
d) This method can be applied to even large sized sequences
5. Which of the following does not describe global alignment algorithm?
a) In initialization step, the first row and first column are subject to gap penalty
b) Score can be negative
c) In trace back step, beginning is with the cell at the lower right of the matrix and it ends at top left cell
d) First row and first column are set to zero
6. Which of the following does not describe PAM matrices?
a) These matrices are used in optimal alignment scoring
b) It stands for Point Altered Mutations
c) It stands for Point Accepted Mutations
d) It was first developed by Margaret Dayhoff
7. Which of the following is untrue regarding the scoring system used in dynamic programming?
a) If the residues are same in both the sequences the match score is assumed as +5 which is added to the diagonally positioned cell of the current cell
b) If the residues are not same, the mismatch score is assumed as -3
c) If the residues are not same, the mismatch score is assumed as 3
d) The score should be added to the diagonally positioned cell of the current cell
8. Which of the following does not describe global alignment algorithm?
a) Score can be negative in this method
b) It is based on dynamic programming technique
c) For two sequences of length m and n, the matrix to be defined should be of dimensions m+1 and n+1
d) For two sequences of length m and n, the matrix to be defined should be of dimensions m and n
9. Which of the following does not describe global alignment algorithm?
a) It attempts to align every residue in every sequence
b) It is most useful when the aligning sequences are similar and of roughly the same size
c) It is useful when the aligning sequences are dissimilar
d) It can use Needleman-Wunsch algorithm
10. Which of the following is wrong in case of substitution matrices?
a) They determine likelihood of homology between two sequences
b) They use system where substitutions that are more likely should get a higher score
c) They use system where substitutions that are less likely should get a lower score
d) BLOSUM-X type uses logarithmic identity to find similarity
1. Which of the following is untrue regarding Progressive Alignment Method?
a) Progressive alignment depends on the stepwise assembly of multiple alignment and is heuristic in nature
b) It speeds up the alignment of multiple sequences through a multistep process
c) It first conducts pair wise alignments for each possible pair of sequences using the Needleman–Wunsch global alignment method and records these similarity scores from the pair wise comparisons
d) Its drawback is it slows down the alignment of multiple sequences through a single step process
2. Clustal is a progressive multiple alignment program available either as a stand-alone or on-line program.
3. Which of the following is untrue regarding the progressive alignment method?
a) The program also applies a weighting scheme to increase the reliability of aligning divergent sequences (sequences with less than 25% identity)
b) The progress is done by down weighting redundant and closely related groups of sequences in the alignment by a certain factor
c) This scheme is useful in enhancing similar sequences from dominating the alignment
d) This scheme is useful in enhancing similar sequences from dominating the alignment
4. Which of the following is not a drawback of the progressive alignment method?
a) The progressive alignment method is not suitable for comparing sequences of different lengths because it is a global alignment–based method
b) In this method the use of affine gap penalties, long gaps are not allowed, and, in some cases, this may limit the accuracy of the method
c) In this method the use of affine gap penalties, long gaps is allowed, and, in some cases, this may limit the accuracy of the method
d) The final alignment result is also influenced by the order of sequence addition
5. Which of the following is untrue regarding T-Coffee?
a) It stands for Tree-based Consistency Objective Function for alignment Evaluation
b) It performs progressive sequence alignments as in Clustal.
c) The global pair wise alignment is not performed using the Clustal program.
d) The local pair wise alignment is generated by the Lalign program, from which the top ten scored alignments are selected
6. Which of the following is untrue about iterative approach?
a) The iterative approach is based on the idea that an optimal solution can be found by repeatedly modifying existing suboptimal solutions
b) Because the order of the sequences used for alignment is different in each iteration
c) This method is also heuristic in nature and does not have guarantees for finding the optimal alignment
d) This method is not based on heuristic methods
7. Which of the following is untrue about PRRN?
a) PRRN is a web-based program that uses a double nested iterative strategy for multiple alignment
b) It performs multiple alignments through two sets of iterations: inner iteration and outer iteration
c) In the outer iteration, an initial random alignment is generated that is used to derive a UPGMA tree
d) In the inner iteration, the sequences are randomly divided into multiple groups
8. The major drawback of the progressive and iterative alignment strategies is that they are largely global alignment based and may therefore fail to recognize conserved domains and motifs among highly divergent sequences of varying lengths.
9. Which of the following is untrue about DIALIGN2?
a) It is a web based program designed to detect local similarities
b) It is designed to detect global similarities
c) It does not apply gap penalties and thus is not sensitive to long gaps
d) The method breaks each of the sequences down to smaller segments and performs all possible pair wise alignments between the segments
10. Match-Box compares segments of some of the nine residues of possible Pair wise alignments.
1. Which of the following is incorrect about the RNA structure prediction?
a) Given the sequence, it provides an ab initio prediction of secondary structure
b) From the many possible choices of complementary sequences that can potentially base-pair, the compatible sets that provide the highest energy molecules are chosen
c) Structures with energies almost as stable as the most stable one may also be produced
d) Regions whose predictions are the most reliable can be identified from such an analysis
2. A type of RNA secondary structure prediction method takes into account conserved patterns of base-pairing that are conserved during evolution of a given class of RNA molecules.
3. RNA secondary structure is composed primarily of triple-stranded RNA regions formed by folding the single-stranded molecule back twice on itself.
4. ____ wobble pairs may be produced in these double-stranded regions.
5. In predicting RNA secondary structure, some simplifying assumptions are usually made, like–the _____ structure is similar to the _____
a) most likely, energetically most unstable structure
b) most unlikely, energetically most stable structure
c) most likely, energetically most stable structure
d) least likely, energetically most stable structure
6. 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.
b) not at all
7. 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 ________
a) crossing, produces knots
b) crossing, does not produce any knots
c) folding, produces knots
d) folding, does not produce any knots
8. Martinez (1984) made a list of possible double-stranded regions, and these regions were then given weights in proportion to their equilibrium constants, calculated by ______
a) the Boltzmann function [ exp (-∆G/RT2) ].
b) the Boltzmann function [ exp (-∆G/RT) ].
c) the Boltzmann function [ exp (-∆G/RT -T) ].
d) the Boltzmann function [ exp (∆G/RT) ].
9. In 1971, first estimation of the energy associated with regions of secondary structure by extrapolation from studies with small molecules was done and then attempt was made to predict which configurations of larger molecules were the most energetically stable.
10. Nussinov and Jacobson (1980) were the first to design a precise and efficient algorithm for predicting secondary structure.
1. When did Smith–Waterman first describe the algorithm for local alignment?
2. Which of the following does not describe local alignment?
a) A local alignment aligns a substring of the query sequence to a substring of the target sequence
b) A local alignment is defined by maximizing the alignment score, so that deleting a column from either end would reduce the score, and adding further columns at either end would also reduce the score
c) Local alignments have terminal gaps
d) The substrings to be examined may be all of one or both sequences; if all of both are included then the local alignment is also global
3. Which of the following does not describe local alignment algorithm?
a) Score can be negative
b) Negative score is set to 0
c) First row and first column are set to 0 in initialization step
d) In traceback step, beginning is with the highest score, it ends when 0 is encountered
4. Local alignments are more used when_____________
a) There are totally similar and equal length sequences
b) Dissimilar sequences are suspected to contain regions of similarity
c) Similar sequence motif with larger sequence context
d) Partially similar, different length and conserved region containing sequences
5. Which of the following does not describe BLOSUM matrices?
a) It stands for BLOcks SUbstitution Matrix
b) It was developed by Henikoff and Henikoff
c) The year it was developed was 1992
d) These matrices are logarithmic identity values
6. 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)
7. Among the following which one is not the approach to the local alignment?
a) Smith–Waterman algorithm
b) K-tuple method
c) Words method
d) Needleman-Wunsch algorithm
8. Which of the following does not describe k-tuple methods?
a) k-tuple methods are best known for their implementation in the database search tools FASTA and the BLAST family
b) They are also known as words methods
c) They are basically heuristic methods to find local alignment
d) They are useful in small scale databases
9. Which of the following does not describe BLAST?
a) It stands for Basic Local Alignment Search Tool
b) It uses word matching like FASTA
c) It is one of the tools of the NCBI
d) Even if no words are similar, there is an alignment to be considered
10. Which of the following is untrue regarding BLAST and FASTA?
a) FASTA is faster than BLAST
b) FASTA is the most accurate
c) BLAST has limited choices of databases
d) FASTA is more sensitive for DNA-DNA comparisons