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MCQOPTIONS
This section includes 151 Mcqs, each offering curated multiple-choice questions to sharpen your Bioinformatics knowledge and support exam preparation. Choose a topic below to get started.
| 101. |
Which of the following is not a characteristic of Fuzzy or approximate matches in regular expression? |
| A. | This method is able to include more variant forms of a motif with a conserved function |
| B. | the rule of matching is based on observations, not actual assumptions |
| C. | with the more relaxed matching, there is increase of the noise level and false positives |
| D. | the rule of matching is based on assumptions not actual observations |
| Answer» C. with the more relaxed matching, there is increase of the noise level and false positives | |
| 102. |
What does this representation mean- R.L.[EQD]? |
| A. | An arginine- Amino acid- Leucine- Amino acid- Either Apartic acid, glutamic acid or glutamine |
| B. | An arginine- Leucine- Either Apartic acid, glutamic acid or glutamine |
| C. | An arginine- Leucine- Amino acid- Either Apartic acid, glutamic acid or glutamine |
| D. | An arginine- Leucine- Apartic acid and glutamic acid and glutamine |
| Answer» B. An arginine- Leucine- Either Apartic acid, glutamic acid or glutamine | |
| 103. |
Emotif uses which databases for alignment of sequences? |
| A. | BLOCKS and PRINTS databases |
| B. | PROSITE |
| C. | BLOCKS |
| D. | PRINTS |
| Answer» B. PROSITE | |
| 104. |
While analysing motif sequences, what is the major disadvantageous feature of PROSITE? |
| A. | The database constructs profiles to complement some of the sequence patterns |
| B. | The functional information of these patterns is primarily based on published literature |
| C. | Some of the sequence patterns are too short to be specific |
| D. | Lack of specificity about probability and variation and relation between them |
| Answer» D. Lack of specificity about probability and variation and relation between them | |
| 105. |
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 |
| Answer» E. | |
| 106. |
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 |
| Answer» C. It stands for Point Accepted Mutations | |
| 107. |
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 |
| Answer» D. The score should be added to the diagonally positioned cell of the current cell | |
| 108. |
Which of the following best defines regular expressions? |
| A. | They are made up of terms, operators and modifiers |
| B. | They describe string or set of strings to find matching patterns |
| C. | They are strictly restricted to alignment and corresponding score |
| D. | They consist of set of rules for the connotations of various amino acid residues |
| Answer» C. They are strictly restricted to alignment and corresponding score | |
| 109. |
While scanning for similarities in motifs, how regular expressions’ techniques work? |
| A. | It represents a sequence family by a string of characters and further compares them |
| B. | An algorithm similar to dynamic programming is used |
| C. | Dot matrix analysis is used in this type of sequence analysis |
| D. | Matrix analysis methods are used in this type |
| Answer» B. An algorithm similar to dynamic programming is used | |
| 110. |
In terminologies related to regular expressions which of the following is false about terms and operators? |
| A. | Terms are strings or substrings |
| B. | Operators combine terms and expressions |
| C. | Operators do not have precedence |
| D. | Operators have precedence like arithmetic operators |
| Answer» D. Operators have precedence like arithmetic operators | |
| 111. |
In regular expressions, which of the following pair of pattern is wrongly matched with its significance? |
| A. | ‘-’ – separator |
| B. | < – N-terminal |
| C. | > – C-terminal |
| D. | ‘>>’ – end |
| Answer» E. | |
| 112. |
Point out the wrong or irrelevant mathematical method in motif analysis. |
| A. | Enumeration |
| B. | Probabilistic Optimization |
| C. | Deterministic Optimization |
| D. | Literature mining |
| Answer» E. | |
| 113. |
Which of the following is false in case of the database InterPro and its algorithm? |
| A. | InterPro is an integrated pattern database designed to unify multiple databases for protein domains and functional sites |
| B. | This database integrates information from PROSITE, Pfam, PRINTS, ProDom, and SMART databases |
| C. | Only overlapping motifs and domains in a protein sequence derived by all five databases are included |
| D. | All the motifs and domains in a protein sequence derived by all five databases are included |
| Answer» E. | |
| 114. |
Which of the following is false in case of the CDART and its algorithm? |
| A. | CDART is a domain search program that combines the results from RPS-BLAST, SMART, and Pfam |
| B. | The program is now an integral part of the regular BLAST search function |
| C. | CDART is a substitute for individual database searches |
| D. | It stands for Conserved Domain Architecture |
| Answer» D. It stands for Conserved Domain Architecture | |
| 115. |
Which of the following is false in case of the database Pfam and its algorithm? |
| A. | Each motif or domain is represented by an HMM profile generated from the seed alignment of a number of conserved homologous proteins |
| B. | Since the probability scoring mechanism is more complex in HMM than in a profile-based approach the use of HMM yields further increases in sensitivity of the database matches |
| C. | Pfam-B only contains sequence families not covered in Pfam |
| D. | The functional annotation of motifs in Pfam-A is often related to that in UNIPROT |
| Answer» E. | |
| 116. |
Which of the following is false in case of the database SMART and its algorithm? |
| A. | Contains HMM profiles constructed from manually refined protein domain alignments |
| B. | Alignments in the database are built based on tertiary structures whenever available or based on PSI-BLAST profiles |
| C. | Alignments are further checked but not refined by human annotators before HMM profile construction |
| D. | SMART stands for Simple Modular Architecture Research Tool |
| Answer» D. SMART stands for Simple Modular Architecture Research Tool | |
| 117. |
Which of the following statements about CATH-Gene3D and HAMAP databases is incorrect regarding its features? |
| A. | CATH-Gene3D describes protein families and domain architectures in complete genomes |
| B. | In CATH-Gene3D the functional annotation is provided to proteins from single resource |
| C. | HAMAP profiles are manually created by expert curators they identify proteins that are part of well-conserved bacterial, archaeal and plastid-encoded proteins families or subfamilies. |
| D. | HAMAP stands for High-quality Automated and Manual Annotation of microbial Proteomes |
| Answer» C. HAMAP profiles are manually created by expert curators they identify proteins that are part of well-conserved bacterial, archaeal and plastid-encoded proteins families or subfamilies. | |
| 118. |
Which of the following statements about PRINTS and ProDom databases is incorrect regarding its features? |
| A. | PRINTS is a compendium of protein fingerprints |
| B. | Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space |
| C. | Current versions of ProDom are built using a novel procedure based on recursive BLAST searches |
| D. | ProDom domain database consists of an automatic compilation of homologous domains |
| Answer» D. ProDom domain database consists of an automatic compilation of homologous domains | |
| 119. |
Which of the following statements about PANTHER and TIGRFAMs databases is incorrect regarding its features? |
| A. | TIGRFAMs provides a tool for identifying functionally related proteins based on sequence homology |
| B. | TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, hidden Markov models (HMMs) and annotation |
| C. | Hidden Markov models (HMMs) are not used in PANTHER |
| D. | PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise |
| Answer» D. PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise | |
| 120. |
What is the source of protein structures in SCOP and CATH? |
| A. | Uniprot |
| B. | Protein Data Bank |
| C. | Ensemble |
| D. | InterPro |
| Answer» C. Ensemble | |
| 121. |
Which of the following statements about SUPERFAMILY database is incorrect regarding its features? |
| A. | Sequences can be submitted raw or FASTA format |
| B. | Sequences must be submitted in FASTA format only |
| C. | It searches the database using a superfamily, family, or species name plus a sequence, SCOP, PDB or HMM ID’s |
| D. | It has generated GO annotations for evolutionarily closed domains and distant domains |
| Answer» C. It searches the database using a superfamily, family, or species name plus a sequence, SCOP, PDB or HMM ID’s | |
| 122. |
Which of the following is not an advantage of Statistical models’ methods in analyzing protein motifs? |
| A. | Sequence information is preserved from a multiple sequence alignment and expresses it with probabilistic models |
| B. | Statistical models allow partial matches and compensate for unobserved sequence patterns using pseudo-counts |
| C. | Statistical models have stronger predictive power than the regular expression based approach, even when they are derived from a limited set of sequences |
| D. | The comparative flexibility is less in case of these methods when compared to regular expressions methods |
| Answer» E. | |
| 123. |
Which of the following is not an advantageous feature or algorithm of the database PRINTS? |
| A. | This program breaks down a motif into even smaller non-overlapping units called ‘fingerprints’, which are represented by unweighted PSSMs |
| B. | To define a motif, at least a majority of fingerprints are required to match with a query sequence |
| C. | A query that has simultaneous high-scoring matches to a majority of fingerprints belonging to a motif is a good indication of containing the functional motif |
| D. | The difficulty to recognize short motifs when they reach the size of single fingerprints |
| Answer» E. | |
| 124. |
For motif scanning which of the following programs or databases is for regulated sites curated from scientific literature? |
| A. | ENSEMBL |
| B. | ORegAnno |
| C. | MAST |
| D. | Clover |
| Answer» C. MAST | |
| 125. |
Which of the following is untrue in case of the database BLOCKS? |
| A. | The alignments are automatically generated using the same data sets used for deriving the BLOSUM matrices |
| B. | The derived ungapped alignments are called ‘blocks’, which are usually longer than motifs, are subsequently converted to PSSMs |
| C. | A weighting scheme and pseudo counts are subsequently applied to the PSSMs to account for underrepresented and unobserved residues in alignments |
| D. | The functional annotation of blocks is not consistent with that for the motifs |
| Answer» E. | |
| 126. |
Which of the following statements about InterPro is incorrect regarding its features? |
| A. | Protein relatedness is defined by the P-values from the BLAST alignments |
| B. | The most closely related sequences are grouped into the lowest level clusters |
| C. | More distant protein groups are merged into higher levels of clusters |
| D. | The outcome of this cluster merging is a tree-like structure of functional categories |
| Answer» B. The most closely related sequences are grouped into the lowest level clusters | |
| 127. |
In which of the following multipurpose packages Gibbs sampling algorithm is used? |
| A. | Consensus |
| B. | BEST |
| C. | AlignACE |
| D. | PhyloCon |
| Answer» D. PhyloCon | |
| 128. |
Which of the following statements about COG is incorrect regarding its features? |
| A. | Currently, there are 4,873 clusters in the COG databases derived from unicellular organisms |
| B. | It is constructed by comparing protein sequences encoded in forty-three completely sequenced genomes, which are mainly from prokaryotes, representing thirty major phylogenetic lineages |
| C. | The interface for sequence searching in the COG database is the COGnitor program, which is based on gapped BLAST |
| D. | It is a protein family database based on structural classification |
| Answer» E. | |
| 129. |
Which of the following is not a member database of InterPro? |
| A. | SCOP |
| B. | HAMAP |
| C. | PANTHER |
| D. | Pfam |
| Answer» B. HAMAP | |
| 130. |
Pfam is available at four locations around the world. Which of the following is not one of them? |
| A. | UK |
| B. | Sweden |
| C. | US |
| D. | Japan |
| Answer» E. | |
| 131. |
Which of the following statements about SCOP is incorrect regarding its features? |
| A. | Proteins with the same shapes but having little sequence or functional similarity are placed in different super families, and are assumed to have only a very distant common ancestor |
| B. | Proteins having the same shape and some similarity of sequence and/or function are placed in ‘families’, and are assumed to have a closer common ancestor |
| C. | SCOP was created in 1994 in the Centre of Protein Engineering and the University College London |
| D. | It aims to determine the evolutionary relationship between proteins |
| Answer» D. It aims to determine the evolutionary relationship between proteins | |
| 132. |
When did Needleman-Wunsch first describe the algorithm for global alignment? |
| A. | 1899 |
| B. | 1970 |
| C. | 1930 |
| D. | 1950 |
| Answer» C. 1930 | |
| 133. |
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 |
| Answer» E. | |
| 134. |
Which of the following is not an advantage of Needleman-Wunsch algorithm? |
| A. | New algorithmic improvements as well as increasing computer capacity make it 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 |
| Answer» 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 | |
| 135. |
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 |
| Answer» E. | |
| 136. |
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 |
| Answer» E. | |
| 137. |
What is the length of a motif, in terms of amino acids residue? |
| A. | 30- 60 |
| B. | 10- 20 |
| C. | 70- 90 |
| D. | 1- 10 |
| Answer» C. 70- 90 | |
| 138. |
Which of the following is false about the ‘loop’ structure in proteins? |
| A. | They connect helices and sheets |
| B. | They are more tolerant of mutations |
| C. | They are more flexible and can adopt multiple conformations |
| D. | They are never the components of active sites |
| Answer» E. | |
| 139. |
On average, what is the length of a typical domain? |
| A. | About 100 residues |
| B. | About 300 residues |
| C. | About 500 residues |
| D. | About 900 residues |
| Answer» B. About 300 residues | |
| 140. |
Which of the following least describes Long Loop β-hairpins? |
| A. | They are Often referred to as a ‘random coil’ conformation |
| B. | Generally they are referred to as the β-meander supersecondary structure |
| C. | Loop looks similar to the Greek Letter Ω |
| D. | Wide-range of conformations with very specific sequence preferences |
| Answer» E. | |
| 141. |
Which of the common structural motifs are described wrongly? |
| A. | β-hairpin – adjacent antiparallel strands |
| B. | Greek key – 4 adjacent antiparallel strand |
| C. | β-α-β – 2 parallel strands connected by helix |
| D. | β-α-β – 2 antiparallel strands connected by helix |
| Answer» E. | |
| 142. |
WHICH_OF_THE_FOLLOWING_IS_UNTRUE_ABOUT_THE_PRSS_PROGRAM??$ |
| A. | It stands for Probability of Random Shuffles |
| B. | It is a web-based program that can be used to evaluate the statistical significance of DNA or protein sequence alignment |
| C. | It first aligns two sequences using the Needleman-Wunsch algorithm and calculates the score |
| D. | It holds one sequence in its original form and randomizes the order of residues in the other sequence. |
| Answer» D. It holds one sequence in its original form and randomizes the order of residues in the other sequence. | |
| 143. |
The_major_disadvantage_of_the_PRSS_program_is_that_it_doesn’t_allow_partial_shuffling.$# |
| A. | True |
| B. | False |
| Answer» C. | |
| 144. |
It is not known whether the Gumble distribution applies equally well to gapped alignments? |
| A. | True |
| B. | False |
| Answer» B. False | |
| 145. |
If the score is located in the extreme margin of the distribution, that means that the alignment between the two sequences is ______ due to random chance and is thus considered ______ |
| A. | unlikely, significant |
| B. | unlikely, insignificant |
| C. | unlikely, insignificant |
| D. | very likely, significant |
| Answer» B. unlikely, insignificant | |
| 146. |
What is used to generate parameters for the extreme distribution? |
| A. | The pool of alignment scores from the shuffled sequences |
| B. | A single score of a shuffled sequence |
| C. | The pool of alignment scores from the unshuffled sequences |
| D. | The basic optimal score computed at the beginning of the test |
| Answer» B. A single score of a shuffled sequence | |
| 147. |
In the statistical test, randomization process in which one of the two given sequences is randomly shuffled. |
| A. | True |
| B. | False |
| Answer» B. False | |
| 148. |
Which of the following is a part of the statistical test of sequences? |
| A. | An optimal alignment between two chosen sequences is obtained at the end |
| B. | Unrelated sequences of the same length are then generated through a randomization process |
| C. | Unrelated sequences of the different length are then generated through a randomization process |
| D. | Related sequences of the same length are then generated through a randomization process |
| Answer» C. Unrelated sequences of the different length are then generated through a randomization process | |
| 149. |
Many studies have demonstrated that the distribution of similarity scores assumes a peculiar shape that resembles a highly skewed normal distribution with a long tail on one side. The distribution matches the _______ |
| A. | Gumble elective value distribution |
| B. | Gumble extreme void distribution |
| C. | Gumble end value distribution |
| D. | Gumble extreme value distribution |
| Answer» E. | |
| 150. |
By calculating alignment scores of a large number of ______ sequence pairs, a distribution model of the ______ sequence scores can be derived. |
| A. | related, randomized |
| B. | unrelated, randomized |
| C. | unrelated, unrandomized |
| D. | related, unrandomized |
| Answer» C. unrelated, unrandomized | |