Here are 1000 MCQs on Bioinformatics (Chapterwise).
1. Which of the following is untrue regarding the transmembrane proteins?
a) The membrane proteins are also of tremendous biomedical importance
b) They are not drug targets or receptors
c) They are responsible for performing a wide variety of important functions in a cell, such as signal transduction, cross-membrane transport, and energy conversion
d) Constitute up to 30% of all cellular proteins
View Answer
Explanation: The membrane proteins are also of tremendous biomedical importance, as they often serve as drug targets for pharmaceutical development. There are two types of integral membrane proteins: α-helical type and β-barrel type. Most transmembrane proteins contain solely α-helices, which are found in the cytoplasmic membrane. A few membrane proteins consist of β-strands forming a β- barrel topology, a cylindrical structure composed of antiparallel β-sheets.
2. Which of the following is wrong about National Biomedical Research Foundation/Protein Information Resource Sequence Format?
a) This is different than PIR format
b) The first line includes an initial “>” character followed by a two-letter code such as P for complete sequence or F for the fragment, followed by a 1 or 2 to indicate type of sequence, then a semicolon, then a four- to six-character unique name for the entry
c) The NBRF format is similar to the FASTA sequence format but with significant differences
d) Sequences retrieved from the PIR database are not in this compact format, but in an expanded format with much more information about the sequence
View Answer
Explanation: This sequence format, which is sometimes also called the PIR format. It has been used by the National Biomedical Research Foundation/Protein Information Resource (NBRF) and also by other sequence analysis programs.
3. Which of the following is incorrect about ENTREZ?
a) It provides a series of forms that can be filled out to retrieve a Medline reference related to the molecular biology sequence databases
b) It provides a series of forms that can be filled out to retrieve a DNA or protein sequence
c) It is a resource prepared only by the staff of the National Center for Biotechnology Information
d) One straightforward way to access the sequence databases is through ENTREZ
View Answer
Explanation: It is a resource prepared by the staff of the National Center for Biotechnology Information and National Library of Medicine, Bethesda, Maryland. After search for either a protein or a DNA sequence is chosen at the above address, another Web page is provided with a form to fill out for the search.
4. In medical applications, the ultimate goal of gene mapping is to disease genes.
a) False
b) True
View Answer
Explanation: Once the gene is cloned, the determination of DNA sequence is possible. Further, the study of target protein is carried out.
5. Which of the following does not describe local alignment algorithm?
a) In traceback step, beginning is with the highest score, it ends when 0 is encountered
b) First row and first column are set to 0 in initialization step
c) Score can be negative
d) Negative score is set to 0
View Answer
Explanation: Score can be negative. When any element has a score lower than zero, it means that the sequences up to this position have no similarities; this element will then be set to zero to eliminate influence from previous alignment. In this way, calculation can continue to find alignment in any position afterward.
6. Which of the following is an abbreviation of MEME?
a) Multiple Expectation Maximization for Motif Extraction
b) Mega Expectation Maximization for Motif Elicitation
c) Micro Expectation Maximization for Motif Extraction
d) Multiple Expectation Maximization for Motif Elicitation
View Answer
Explanation: 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 modified EM algorithm to avoid the local minimum problem.
7. Which of the following is not a software for dot plot analysis?
a) DOTMATCHER
b) LALIGN
c) DOTLET
d) SIMMI
View Answer
Explanation: For the purpose of dot plot interpretation there are various softwares currently present. Among these SIM is used for these kinds of alignments through dot-plot method that is wrongly abbreviated.
8. Which of the following is not a site on internet for alignment of sequence pairs?
a) BLASTN
b) BCM Search Launcher
c) BLASTX
d) SIM
View Answer
Explanation: BLASTP is used under BLAST 2 sequence alignment. Also, The BLAST algorithm normally used for database similarity searches can also be used to align two sequences. SIM is known as Local similarity program for finding alternative alignments.
9. Which of the following is true regarding the assumptions in the method of constructing the Dayhoff scoring matrix?
a) sites do not vary in their degree of mutability
b) it is assumed that each amino acid position is equally mutable
c) it is assumed that each amino acid position is not equally mutable
d) it is assumed that each amino acid position is not mutable at all
View Answer
Explanation: In this process, first, it is assumed that each amino acid position is equally mutable, whereas, in fact, sites vary considerably in their degree of mutability. Mutagenesis hot spots are well known in molecular genetics, and variations in the mutability of different amino acid sites in proteins are well known.
10. Which of the following feature of Bayesian methods is the disadvantage?
a) A specific mutational model is required
b) Computationally Bayesian methods are better
c) A length and distance that gives the highest overall probability may be determined
d) They are used to calculate evolutionary distance
View Answer
Explanation: One disadvantage of the Bayesian approach is that a specific mutational model is required, whereas other methods, such as the maximum likelihood approach, can be used to estimate the best mutational model as well as the distance. Computationally, however, the Bayesian method is much more practical.
11. Which of the following is incorrect regarding sequence homology?
a) It is an important concept in sequence analysis
b) When two sequences are descended from a common evolutionary origin, they are said to share homology
c) Two sequences can homologous relationship even if have do not have common origin
d) When two sequences are descended from a common evolutionary origin, they are said to have a homologous relationship
View Answer
Explanation: Homologous relationships are more certain when the sequences have common evolutionary origin. A related but different term is sequence similarity, which is the percentage of aligned residues that are similar in physiochemical properties such as size, charge, and hydrophobicity.
12. The presence of evolutionary traces is because some of the residues that perform key functional and structural roles tend to be preserved by natural selection; other residues that may be less crucial for structure and function tend to mutate more frequently.
a) True
b) False
View Answer
Explanation: The residues that perform key functional and structural roles tend to be preserved by natural selection. For example, active site residues of an enzyme family tend to be conserved because they are responsible for catalytic functions. Therefore, by comparing sequences through alignment, patterns of conservation and variation can be identified.
13. A sequence can be aligned with itself to identify internal repeat elements.
a) True
b) False
View Answer
Explanation: In the self comparison, there is a main diagonal for perfect matching of each residue. If repeats are present, short parallel lines are observed above and below the main diagonal.
14. What is used to generate parameters for the extreme distribution?
a) The pool of alignment scores from the unshuffled sequences
b) The pool of alignment scores from the shuffled sequences
c) The basic optimal score computed at the beginning of the test
d) A single score of a shuffled sequence
View Answer
Explanation: Maximum scores are obtained through repeated shuffling. Then the pool of alignment scores from the shuffled sequences is used to generate parameters for the extreme distribution. The original alignment score is then compared against the distribution of random alignments to determine whether the score is beyond random chance.
15. The major disadvantage of the PRSS program is that it doesn’t allow partial shuffling.
a) True
b) False
View Answer
Explanation: The major feature of the program is that it allows partial shuffling. For example, shuffling can be restricted to residues within a local window of 25–40, whereas the residues outside the window remain unchanged.
16. Which of the following scores are not considered while calculating the SP scores?
a) Number of gap penalties
b) All possible pair wise matches
c) All possible mismatches
d) All possible gap costs
View Answer
Explanation: In calculating the SP scores, each column is scored by summing the scores for all possible pair wise matches, mismatches and gap costs. The score of the entire alignment is the sum of all of the column scores. The score of the entire alignment is the sum of all of the column scores. In that case, option d becomes an irrelevant choice here.
17. Which of the following is untrue about the iterative approach?
a) Because the order of the sequences used for alignment is different in each iteration
b) This method is not based on heuristic methods
c) The iterative approach is based on the idea that an optimal solution can be found by repeatedly modifying existing suboptimal solutions
d) This method is also heuristic in nature and does not have guarantees for finding the optimal alignment
View Answer
Explanation: This method is based on heuristic methods. The procedure starts by producing a low-quality alignment and gradually improves it by iterative realignment through well-defined procedures until no more improvements in the alignment scores can be achieved.
18. Which of the following is not the objective to perform sequence comparison?
a) To find the common motifs present in both sequences
b) To study the physical properties of molecules
c) To study evolutionary relationships
d) To observe patterns of conservation
View Answer
Explanation: To assess whether it is likely that two sequences evolved from the same sequence comparison is required. Also, to find out which sequences from the database are similar to the sequence at hand, sequence comparison is carried out.
19. The initial alignments used to produce the guide tree may be obtained by various methods. Which of the following is not one of them?
a) pattern-finding approach similar
b) FASTA
c) Faster, full dynamic programming method
d) Fast k-tuple
View Answer
Explanation: The methods used, might be fast k-tuple or pattern-finding approach similar to FASTA that is useful for many sequences and the full dynamic programming method as well. But the option d becomes incorrect as full dynamic programming method is slower as compared to rest of the methods in options.
20. In Genetic Algorithm, in the mutation process _______
a) sequence is not changed
b) sequence is changed
c) gaps are not rearranged
d) gaps are not inserted
View Answer
Explanation: In the mutation process, the sequence is not changed (else it would no longer be an alignment), but gaps are inserted and rearranged in an attempt to create a better-scoring MSA. In the gap insertion process, the sequences in a given MSA are divided into two groups based on an estimated phylogenetic tree, and gaps of random length are inserted into random positions in the alignment.
21. Which of the following is not among the methods for finding localized sequence similarity?
a) Extraction of Blocks from a Global or Local MSA
b) Pattern blocking
c) Block Analysis
d) Profile Analysis
View Answer
Explanation: 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.
22. For the 10-residue DNA sequence example, there are _______ possible starting sites for a 20-residue-long site.
a) 70
b) 51
c) 81
d) 40
View Answer
Explanation: For the 10-residue DNA sequence example, there are 100 – 20 +1 possible starting sites for a 20-residue-long site. Where the first one is at position 1 in the sequence ending one at 20 and the last beginning at position 81 and ending at 100 (there is not enough sequence for a 20-residue-long site beyond position 81).
23. MACAW is a local multiple sequence alignment program and a sequence editing tool.
a) True
b) False
View Answer
Explanation: MACAW is both a local multiple sequence alignment program and a sequence editing tool. Given a set of sequences, the program finds ungapped blocks in the sequences and gives their statistical significance. Later versions of the program find blocks by one of three user-chosen methods.
24. Which of the following is not one of the requirements for implementing algorithms for sequence database searching?
a) Speed
b) Size of the dataset
c) Sensitivity
d) Specificity
View Answer
Explanation: There are unique requirements for implementing algorithms for sequence database searching out of which, the later three play an important role. However, speed can vary with the size of database. achieving all three at a time is nearly impossible.
25. Which of the following is not a variant of BLAST?
a) BLASTX
b) TBLASTNX
c) BLASTP
d) BLASTN
View Answer
Explanation: BLAST is a family of programs that includes BLASTN, BLASTP, BLASTX TBLASTN, and TBLASTX. BLASTN queries nucleotide sequences with a nucleotide sequence database. The alignment scoring is based on the BLOSUM62 matrix.
26. Which of the following is not correct about FASTA?
a) It was in fact the first database similarity search tool developed, preceding the development of BLAST
b) FASTA uses a ‘hashing’ strategy to find matches for a short stretch of identical residues with a length of k
c) The string of residues is known as blocks
d) Its stands for FAST ALL
View Answer
Explanation: The string of residues is known as ktuples or ktups, which are equivalent to words inBLAST, but are normally shorter than the words. Typically, a ktup is composed of two residues for protein sequences and six residues for DNA sequences.
27. Which of the following is not a benefit of BLAST?
a) Speed
b) Statistical rigor
c) Handling of gaps
d) More sensitive
View Answer
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.
28. Which of the following is not correct about the Coils and Loops?
a) They are irregular structures
b) If the connecting regions are completely irregular, they belong to random coils
c) They are regular structures
d) The loops are often characterized by sharp turns or hairpin-like structures
View Answer
Explanation: Residues in the loop or coil regions tend to be charged and polar and located on the surface of the protein structure. They are often the evolutionarily variable regions where mutations, deletions, and insertions frequently occur. They can be functionally significant because these locations are often the active sites of proteins.
29. Which of the following is an incorrect statement?
a) Molscript is not capable of generating ball-and-stick styles
b) In particular, secondary structure elements can be drawn with solid spirals and arrows representing α-helices and β-strands, respectively
c) Molscript is capable of generating space-filling
d) Molscript is a UNIX program capable of generating wire-frame
View Answer
Explanation: Visually appealing images can be generated that are of publication quality. The drawback is that the program is command-line–based and not very user friendly. A modified UNIX program called Bobscript is available with enhanced features.
30. Which of the following is untrue about SCOP?
a) It is constructed almost entirely based on manual examination of protein structures
b) The SCOP families consist of proteins having low sequence identity (>30%)
c) It is a database for comparing and classifying protein structures
d) The proteins are grouped into hierarchies of classes, folds, superfamilies, and families
View Answer
Explanation: The SCOP families consist of proteins having high sequence identity (>30%). Thus, the proteins within a family clearly share close evolutionary relationships and normally have the same functionality. The protein structures at this level are also extremely similar.
31. Which of the following is untrue regarding Prediction with Neural Networks?
a) A neural network is trained by a single sequence
b) When the sufficiently trained network processes an unknown sequence, it applies the rules learned in training to recognize particular structural patterns
c) When multiple sequence alignments and neural networks are combined, the result is further improved accuracy
d) A neural network is trained by a sequence profile derived from the multiple sequence alignment
View Answer
Explanation: A neural network is trained not by a single sequence but by a sequence profile derived from the multiple sequence alignment. This combined approach has been shown to improve the accuracy to above 75%, which is a breakthrough in secondary structure prediction. The improvement mainly comes from enhanced secondary structure signals through consensus drawing. The following lists several frequently used third-generation prediction algorithms available as web servers.
32. Which of the following is true regarding Coiled coil?
a) They have an integral repeat of seven residues
b) They have an integral repeat of thirty residues
c) The sequence periodicity doesn’t contribute in designing algorithms to predict the structural domain
d) They have an integral repeat of twenty residues
View Answer
Explanation: Coiled coils have an integral repeat of seven residues (heptads) which assume a side-chain packing geometry at facing residues. For every seven residues, the first and fourth are hydrophobic, facing the helical interface; the others are hydrophilic and exposed to the solvent. The sequence periodicity forms the basis for designing algorithms to predict this important structural domain.
33. Which of the following is untrue regarding Chou–Fasman and GOR methods?
a) They suffer from the fact that the prediction rules are somewhat arbitrary
b) They are based on single sequence statistics with clear relation to known protein-folding theories
c) They are developed in the 1970s
d) Both are the first-generation methods
View Answer
Explanation: They are based on single sequence statistics without clear relation to known protein-folding theories. The predictions solely rely on local sequence information and fail to take into account long range interactions. A Chou-Fasman–based prediction does not even consider the short-range environmental information.
34. Which of the following is untrue about homology modeling?
a) It doesn’t involve the evolutionary distances anywhere
b) The principle behind it is that if two proteins share a high enough sequence similarity, they are likely to have very similar three-dimensional structures
c) Homology modeling predicts protein structures based on sequence homology with known structures
d) It is also known as comparative modeling
View Answer
Explanation: As the name suggests, homology modeling predicts protein structures based on sequence homology with known structures. Homology modeling produces an all-atom model based on alignment with template proteins.
35. In the pairwise energy based method, a protein sequence is searched for in a structural fold database to find the best matching structural fold using ______ criteria.
a) energy-based
b) residue-based
c) structure-based
d) sequence-based
View Answer
Explanation: The detailed procedure involves aligning the query sequence with each structural fold in a fold library. The alignment is performed essentially at the sequence profile level using dynamic programming or heuristic approaches. Local alignment is often adjusted to get lower energy and thus better fitting. The adjustment can be achieved using algorithms such as double-dynamic programming.
36. Which of the following is untrue about Loop Modeling Step?
a) The gaps cannot be directly modeled
b) Loop modeling is required for closing the gaps requires
c) In the sequence alignment for modeling, there are no regions producing gaps in sequence alignment
d) In the sequence alignment for modeling, there are often regions caused by insertions and deletions producing gaps in sequence alignment
View Answer
Explanation: Closing the gaps requires loop modeling, which is a very difficult problem in homology modeling and is also a major source of error. Loop modeling can be considered a mini–protein modeling problem by itself. Unfortunately, there are no mature methods available that can model loops reliably. Currently, there are two main techniques used to approach the problem: the database searching method and the ab initio method.
37. Which of the following is not a form of RNA?
a) tRNA
b) rRNA
c) mRNA
d) qRNA
View Answer
Explanation: It is known that RNA is a carrier of genetic information and exists in three main forms. They are messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Their main roles are as follows: mRNA is responsible for directing protein synthesis; rRNA provides structural scaffolding within ribosomes; and tRNA serves as a carrier of amino acids for polypeptide synthesis.
Chapterwise Multiple Choice Questions on Bioinformatics
- Sequence Alignment
- Pairwise Sequence Alignment
- Multiple Sequence Alignment
- Database Similarity Searching
- Structural Bioinformatics
- Secondary Structure Prediction
- Protein Tertiary Structure Prediction
- RNA Structure Prediction
- Genome Mapping, Assembly and Comparison
- Functional Genomics & Proteomics
- Molecular Phylogenetics
- Phylogenetic Tree Construction Methods and Programs
- Gene and Promoter Prediction
- Promoter and Regulatory Element Prediction
- Predicting the Structure of Protein – Biomolecular Interactions
- Global Approaches for Studying Protein – Protein Interactions
- Collecting & Storing Sequences in Laboratory
- Genome Analysis
1. Bioinformatics MCQ on Sequence Alignment
The section contains bioinformatics multiple choice questions and answers on protein motfis, motif and domain databases using regular expressions and statistical models, protein family databases, global and local sequence alignment, dot matrix sequence comparison and bayesian statistics.
2. Bioinformatics Multiple Choice Questions on Pairwise Sequence Alignment
The section contains bioinformatics questions and answers on sequence homology versus sequence similarity, methods and statistical significance of sequence alignment.
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3. Bioinformatics MCQ on Multiple Sequence Alignment
The section contains bioinformatics MCQs on exhaustive and heuristic algorithms, wunsch algorithm, progressive and iterative methods of multiple sequence alignment, sequences localized alignment, aiding alignment statistical methods and specific scoring matrices.
4. Bioinformatics Multiple Choice Questions on Database Similarity Searching
The section contains bioinformatics multiple choice questions and answers on heuristic database searching, blast, fasta, smith – waterman method, fasta and blast comparison.
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5. Multiple Choice Questions on Structural Bioinformatics
The section contains bioinformatics questions and answers on protein structure basics and structural visualization, protein structure comparison and classification.
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6. Bioinformatics MCQ on Secondary Structure Prediction
The section contains bioinformatics MCQs on protein secondary structure prediction, secondary structure and coiled coil prediction.
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7. Bioinformatics Multiple Choice Questions on Protein Tertiary Structure Prediction
The section contains bioinformatics multiple choice questions and answers on ab initio protein structural prediction, threading and fold recognition.
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8. Bioinformatics MCQ on RNA Structure Prediction
The section contains bioinformatics questions and answers on rna structures, rna secondary structure prediction methods, ab initio and comparative approach, performance evaluation, prediction limitations, energy method and free grammars, rna genomes and rna structure modeling applications.
9. Bioinformatics Multiple Choice Questions on Genome Mapping, Assembly and Comparison
The section contains bioinformatics MCQs on genome mapping and sequencing, genome sequence assembly, genome annotation and comparative genomics.
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10. Bioinformatics MCQ on Functional Genomics & Proteomics
The section contains bioinformatics multiple choice questions and answers on sequence and microarray based approaches, sage and dna microarrays comparison, protein expression analysis, post translational modification, protein sorting and interactions.
11. Bioinformatics Multiple Choice Questions on Molecular Phylogenetics
The section contains bioinformatics questions and answers on phylogenetics basics, tree representation forms, gene phylogeny versus species phylogeny.
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12. Bioinformatics MCQ on Phylogenetic Tree Construction Methods and Programs
The section contains bioinformatics MCQs on distance and character based methods, phylogenetic tree evaluation and programs, maximum parsimony method, maximum likelihood approach and reliability of phylogenetic predictions.
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13. Bioinformatics Multiple Choice Questions on Gene and Promoter Prediction
The section contains bioinformatics multiple choice questions and answers on gene prediction programs categories, gene prediction in prokaryotes and eukaryotes.
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14. Bioinformatics MCQ on Promoter and Regulatory Element Prediction
The section contains bioinformatics questions and answers on covers prediction algorithms, promoter and regulatory elements in prokaryotes & eukaryotes.
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15. Bioinformatics Multiple Choice Questions on Predicting the Structure of Protein – Biomolecular Interactions
The section contains bioinformatics MCQs on molecular complementarity, conformational flexibility, evaluation of models & visualization methods.
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16. Bioinformatics MCQ on Global Approaches for Studying Protein – Protein Interactions
The section contains bioinformatics multiple choice questions and answers on protein and domain interactions, gene order use and phylogeny to predict protein.
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17. Bioinformatics Multiple Choice Questions on Collecting & Storing Sequences in Laboratory
The section contains bioinformatics questions and answers on dna and genomic sequencing, cdna libraries of expressed genes, sequence formats and storage, database access program, genemo anatomy, comparative genomics, sequence assembly and gene identification.
18. Bioinformatics MCQ on Genome Analysis
The section contains bioinformatics MCQs on genes functional classification, global gene regulation and gene function prediction.
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Wish you the best in your endeavor to learn and master Bioinformatics!
