Bioinformatics Quiz: Test Your Knowledge of Bioinformatics

November 20, 2014

[BIOINFORMATICS QUIZ: TEST YOUR BIOINFORMATICS ]

Which of the following statements is false when describing SWISS-PROT ? a) b) c) d)

It is a curated protein sequence database Data is redundant Provides a high level of annotations It is maintained by Swiss Institute of Bioinformatics Bioinformati cs and EBI .

Arrange the the following following in hierarchical hierarchical top to bottom order order as is done done in SCOP: SCOP: a) b) c) d)

Classes, domains, superfamilies, superfamilie s, folds, families. domains, superfamilies, superfamili es, folds, families, classes. superfamilies, superfamilies , folds, families,domains, families,dom ains, classes Classes, folds, superfamilies,f superfamilies,families, amilies, domains

Which of the following cases are commonly used? a) b) c) d)

gap opening penalty = -2, gap extension penalty = -0.5 gap opening penalty = -0.5, gap extension penalty = -2.0. gap opening penalty = -100, gap extension penalty = 0 gap opening penalty = -100, gap extension penalty = -100

For searching a query sequence with a database, which of the following statement is correct? a) b) c) d)

Nucleotide query against a nucleotide sequence database is done by blastp Protein query against a translated nucleotide nucleotide sequence database is done by blastp Translated nucleotide query against a protein database is done by blastx Protein query against a protein database is done by tblastn

Which is the default scoring matrix used in BLAST? a) b) c) d)

PAM62 BLOSUM 62 BLOSUM 60 BLOSUM 80

PAM matrices are derived by noting evolutionary changes in protein sequences that are more than: a) b) c) d)

80% similar 60% similar 40% similar 25% similar

Which alignment is used to predict whether two sequences are homologous or not? a) Local b) Global c) Pair-wise

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d) Multiple In Molecular Dynamics simulation, the dependence is on: a) b) c) d)

only position only momentum both position and momentum either position or momentum

In phylogenetic analysis, maximum likelihood method is chosen when the sequences have: a) b) c) d)

strong similarity local similarity medium level similarity similari ty no clear identifiable similarity

The method of maximum parsimony is also known as: a) b) c) d)

maximum evolution method minimum evolution method zero evolution method moderate evolution method

In Needleman Wunsch algorithm of pairwise alignment of sequences with lengths n and m, the computational time is proportional to: a) b) c) d)

nxm (n+1) x (m+1) n+m n x (m+1)

In a PHYLIP output, the first line is two numbers, what do they indicate? a) b) c) d)

Number of sequences, length of alignment Length of alignment, number of sequences Number of of gaps, number of sequences Number of sequences, number of gaps

BLAT is used to find: a) b) c) d)

regions of higher identity within genomic assemblies regions of higher differences within genomic assemblies folds in a RNA sequence secondary structures in a given protein

Homology modeling may be distinguished from ab initio prediction because: a) Homology modeling requires a model to be built b) Homology modeling requires alignment of a target to a template BY NaVeeNBioinFoRmaTiCs -


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c) Homology modeling is usefully usefully applied to any protein sequence d) The accuracy of homology modeling is independent of the percent identity between the target and the template Molecular Dynamics simulation is carried out for: a) b) c) d)

Obtaining ensemble of structures at physiological condition Obtaining the structure at global energy minimum Fitting prospective drug candidate molecules to a receptor Modeling a protein structure from sequence alone

Threading approaches can be used to: a) b) c) d)

Predict secondary structures of of proteins Build phylogenetic trees Identify distantly related structural homologs of proteins To check the fitness of a modeled protein structure

What is PROSITE? a) b) c) d)

a database of protein structures a database of interacting proteins a database of protein motifs a search tool

Which is the best annotated database? a) b) c) d)

Genbank PDB Prodom Swissprot

If you want literature information, which is the best website to visit? a) b) c) d)

OMIM Entrez PubMed PROSITE

To know the structural similarity between two proteins, the server to use is a) b) c) d)

PRODOM PROSITE TREMBLE DALI

Which of the following databases is derived from mRNA information? a) dbEST BY NaVeeNBioinFoRmaTiCs -


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b) PDB c) OMIM d) HTGS Which of the following amino acids is least mutable according to PAM scoring matrix? a) b) c) d)

Alanine Glutamine Methionine Cysteine

You have two distantly related proteins. Which of the following sets is the best for comparing them? a) b) c) d)

BLOSUM45 or PAM250 BLOSUM45 or PAM1 BLOSUM80 or PAM250 BLOSUM80 or PAM1

In a sequence database of a given size, which of the following expressions is likely to retrieve more matches (X means any amino acid; any of the residues in square brackets can occupy that position)? a) b) c) d)

D-A-V-I-D [DE]-A-V-I-[DE] [DE]-[AVILM]-X-E D-A-V-E

Which alignment is used to predict whether two sequences are homologous or not? a) b) c) d)

Local Global Pair-wise Multiple

In sequence analysis, Twilight zone refers to a) b) c) d)

a zone of domain in a protein sequence a zone of sequence similarity (0-20% identity) but statistically not significant substitutions in sequence a zone of sequence similarity that is statistically statisticall y significant signifi cant

BLOCKS refers to a) b) c) d)

gapped, aligned motif in a multiple sequence alignment ungapped, aligned motif in a multiple sequence alignment coding sequences non-coding sequences



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CpG islands and codon bias are tools used in eukaryotic genomics to identify open reading frames a) b) c) d)

differenti ate between eukaryotic and prokaryotic differentiate DNA sequences Look for DNA-binding domains determine STS

The type of algorithm that GENSCAN tool employs is a) b) c) d)

Neural network Rule-based system Hidden Markovs model Statistics based

BLASTx is used to a) b) c) d)

search a nucleotide database using a nucleotide query search protein database using a protein query search protein database using a translated nucleotide query search translated nucleotide database using a protein query

Which of the following is a retrieval system? a) b) c) d)

Entrez Bioedit Vecscreen Rasmol

The Smith-Waterman algorithm was developed for a) b) c) d)

Local pairwise sequence alignment Global pairwise sequence alignment Multiple sequence alignment Structural alignment

In Molecular Dynamics simulation the dependence is on a) b) c) d)

position only momentum only both position and momentum either position or momentum

Homology modeling involves a) alignment of the target sequence to the sequence of a template structure b) alignment of the target sequence with multiple sequences with no structural information c) ab initio structure prediction



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d) no input of sequence information Which of the following cases are commonly used in sequence alignment? a) b) c) d)

gap opening penalty = -2, gap extension penalty = -0.5 gap opening penalty = -0.5, gap extension penalty = -2 gap opening penalty = -100, gap extension penalty = 0 gap opening penalty = -100, gap extension penalty = -100

CATH database classifies protein domains. CATH stands for a) b) c) d)

Calssified, Advanced, Technology and Homology Automatic Classification Classifica tion of Turns and Helices Class, Architecture, Topology and Homologous superfamily Classification Classific ation of Alpha Trans-membrane Trans-m embrane Helices

Ab initio approaches approaches for prediction prediction of protein protein structure structure utilize a) b) c) d)

sequence similarity similari ty structural similarity both sequence and structural similarity similarit y basic physicochemical principles

To know the structural similarity between two proteins, the server to use is a) b) c) d)

PRODOM PROSITE TREMBLE DALI

Quantitative Structure Activity Relationship (QSAR) is used for a) b) c) d)

Drug design Protein modeling Aligning two sequences Molecular Dynamics simulation

In protein modeling, molecular mechanics force field is used, because a) b) c) d)

it takes less time as compared to others it is more accurate it guarantees global minimum it explicitly represents the electrons in a calculation

A BLAST hit hit with STS STS division of GenBank GenBank helps you you to understand understand a) only location of the sequence in the genome BY NaVeeNBioinFoRmaTiCs -


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b) only expression of the sequence c) both location and expression of the sequence d) first pass survey sequences SUMOplot is a software used to predict a) b) c) d)

succinyl modification modificati on site serine modification modificati on site ubiquitin attachment site hydrophobicity graph

Which of the following plants contain the largest genome? a) b) c) d)

Arabidopsis thaliana Fritillaria assyriaca Zea mays Triticum dicoccum

C in CATH database CATH database stands for a) b) c) d)

Conformation Configuration Classification Conservation

The program used to convert raw sequence output to an ordered list of bases is called a) b) c) d)

Base calling Neural network Local area network artificial network

Which of the following algorithms implements “once a gap, always a gap” policy? a) b) c) d)

ClustalW Needleman & Wunsch Chou & Fasman FASTA

The sequence alignment tool for immunoglobulins, T-cell receptors, and HLA molecules available at the ImMunoGeneTics information system (IMGT) is a) b) c) d)

IMGT/Collier-de-perles IMGT/V-Quest IMGT/Allele-align IMGT/Junction Analysis

Which of the following scoring matrices of proteins is a distance matrix?



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MDM series of matrices BLOSUM series of matrices Conformational Conformational Similarity Weight matrix Genetic Code Matrix

One PAM means one accepted point mutation per a) b) c) d)

102 residues 10 residues 103 residues 104 residues

Which of the following scoring matrices is one of the best to score an alignment of highly conserved protein sequences? a) b) c) d)

BLOSUM 80 or PAM 120 BLOSUM 62 or PAM 250 BLOSUM 30 or PAM 120 BLOSUM 90 or PAM 350

Which one of the following programs is used primarily for submission of complete genomes and batch submission of sequences to GenBank? a) b) c) d)

BankIt Sequin tbl2asn WEBIN

In reconstruction of phylogenetic trees using molecular sequence data, a singleton site in MSA is considered to be a) b) c) d)

an invariant site an informative variable site an uninformati uninformative ve variable site a conserved site

Which of the following identifiers in GenBank changes with sequence revision/updates? a) b) c) d)

Accession GI Date Both a & b

EST division of EMBL database archives data in a) only 5’ to 3’ direction b) only 3’ to 5’ direction c) both 5’ to 3’ and 3’ to 5’ to represent clones from two ends



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d) either 5’ to 3’ or 3’ to 5’ Which of the following methods is used to predict the 3D structure of a protein when it has < 20% of sequence similarity with the available templates? a) b) c) d)

Homology modelling Dynamic programming Fold recognition Progressive protein programming

Which of the following techniques is implemented to locate MUMs in MUMmer algorithm? a) b) c) d)

Suffix tree generation Hash lookup table K-tuple Exact word match

Which one of the following techniques is used for the evaluation of phylogenetic trees? a) b) c) d)

Null hypothesis Bootstrapping Chi-square Probability

NiceProt is a) b) c) d)

Protein sequence database Derived Protein database Protein sequence view Nucleotide sequence view

Higher version of BLOSUM can be used to detect a) b) c) d)

Closely related sequences Distantly related sequences Unrelated sequences Partially related sequences

TBLASTX matches a DNA query sequence, translated into all six reading frames, against a DNA database with a) b) c) d)

No gaps allowed Gaps allowed Gaps depending on the input sequence Gaps depending on the database

Changing which of the following BLAST parameters would tend to yield fewer search results? a) Turning off the low complexity filter BY NaVeeNBioinFoRmaTiCs -


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b) Changing the expected value from 1 to 10 c) Raising the threshold value d) Changing the scoring matrix from PAM30 to PAM70 The Ramachandran map of a protein representation allows you to identify a) b) c) d)

The most stable structure The tertiary allowed structure The sterically disallowed conformatio conformations ns the secondary structure elements

Which information among the following provides the maximum information to do structure based drug design? a) b) c) d)

3D-structure 3D-structur e of a set of of active active compounds 3D-structure 3D-structur e of the target Crystal structure of target-li target-ligand gand complex Primary structure of the target

To display a ligand molecule, one cannot use the rendering style of a) b) c) d)

Stick Ball and stick Ribbon CPK/space filling

What is the difference between RefSeq and GenBank? a) b) c) d)

RefSeq includes publicly available DNA sequences GenBank includes nonredundant curated data GenBank sequences are derived from RefSeq RefSeq sequences are derived from GenBank

Hemoglobin, myoglobin and globin v protein sequences will be stored in PIR-PSD database as a a) b) c) d)

Sub-family Superfamily Group GenPept

The method of maximum parsimony is also known as a) b) c) d)

Maximum evolution method Minimum evolution method Zero evolution method Moderate evolution method



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The biggest problem in predicting protein coding genes from genome sequencing algorithm is that a) b) c) d)

The software is difficult to use The false negative rate is high; many exons are missed The false-positive rate is high; many exons are falsely assigned The false-positive false-posi tive rate is low; many exons have unknown unknown function.

Artificial intelligence technique technique is used to predict secondary structure of globular protein. Which of the following methods uses this technique to predict secondary structures of globular proteins? a) b) c) d)

Chou and Fasman GOR PHD Ab-initio

WebIn is a sequence submission tool provided by a) b) c) d)

NCBI EMBL EBI RCSB

National Center for Biotechnology Information (NCBI) was established on November 4, 1988 as a division of the a) b) c) d)

National Library of Medicine (NLM) National Institutes of Health (NIH) European Bioinformatics Bioinformati cs Institute ExPASy

FASTA was the first database search program that a) b) c) d)

is much faster than Smith-Wat Smith-Waterman erman is much slower than Smith-Waterman Smith-Waterm an sensitivity and speed of the database search with FASTA are directly related calculates similarity similari ty index

Needleman-Wunsch Needleman-W unsch algorithm, is an example of dynamic programming, which does not involve a) b) c) d)

scoring a matrix setting up a matrix local alignment identifying the optimal alignment

RCSB is



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An Information Portal to Protein database database An Information Portal to DNA database An Informat Information ion Portal to Biological Macromolecular Structures An Information Portal Portal to microarray microarra y

To identify the presence of repeats in a protein, the simplest and fastest way is to perform a a) b) c) d)

self dot-plot dot-plot with another protein with same repeats dot-plot with another protein with any repeat BLAST search

Which one of the following best represents the central dogma of Bioinformatics? a) b) c) d)

Sequence-Structure-Function DNA-RNA-Proteins Motifs-domains-Superfamilies Data-Databanks-Data Data-Databanks- Data mining tools

Multiple sequence alignments are NOT used to derive a) b) c) d)

Motifs Primers PSSMs HMMs

Which one of the following matrices can be used to identify distantly related homologs? a) b) c) d)

BLOSUM90 BLOSUM62 BLOSUM45 BLOSUM80

The LIS technique is used in the MUMmer algorithm for a) b) c) d)

Identification Identificatio n of MUMs Sorting of MUMs Alignment of MUMs Tabulating MUMs

The numbers at the internal nodes of a phylogenetic tree indicate a) b) c) d)

Number of times the OTUs were clustered together Number of parsimony sites shared by OTUs Number of of mismatches shared by OTUs Similarity score of OTUs that cluster together

Which one of the following statements is FALSE?



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a) Needleman & Wunsch algorithm is used for global alignment of of pair of sequences. b) There could be several possible local alignments as part of of a global alignment. c) In Needleman & Wunsch algorithm sequences are randomised by keeping length and composition same. d) The terms identity, similarity and homology are expressed as %. Maximum parsimony analysis in the context of molecular phylogeny implies a) b) c) d)

Complex hypotheses are preferred over simpler hypotheses Complex and simple hypothesis need not be considered Simpler hypotheses hypotheses are preferred over complex hypotheses hypotheses Both complex and simple hypotheses are considered, and the one, which which is more suitable to observations is applied

Molecular dynamics differs from molecular mechanics by taking account of the a) b) c) d)

velocities of the constituent particles effect of the solvent medium non-bonded interactions periodic boundary condition

The double-helical structure of DNA was first obtained using a) b) c) d)

Fiber diffraction only Fiber diffractio diffraction n and molecular modeling X-ray diffraction from single single crystals Diffraction from single crystals and molecular modeling

In protein sequence analysis, Twilight zone refers to the evolutionary distance corresponding to about a) b) c) d)

60% identity between between two proteins 90% identity between between two proteins 30% identity between two proteins 85% identity between between two proteins

In a pairwise alignment, an optimal alignment is the one that a) either minimizes the implied number of evolutionary changes or minimizes a particular scoring function. b) either maximizes the implied number of evolutionary changes or minimizes a particular scoring function. c) either minimizes the implied number of evolutionary changes or maximizes a particular scoring function. d) either maximizes the implied number of evolutionary evolutionar y changes or maximizes a particular scoring function.



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Which one of the following proteins can be used as a template for structure prediction by homology modelling? a) b) c) d)

pdb|1TLH|B: Identities = 39/66 (59%), Positives = 51/66 (77%), Expect = 3e-16 pdb|1DQL|H: Identities = 9/15 (60%), Positives = 12/15 (80%), Expect = 9.9 pdb|1L9U|H:Identities pdb|1L9U|H: Identities = 173/333(51%), Positives = 233/333(69%), Expect = 2e-89 pdb|1RP3|A: Identities = 56/206 (27%), Positives = 98/206 (47%), Expect Expect = 2e-05

How many edges meet at every branch node in a phylogenetic tree? a) b) c) d)

1 2 3 4

Which of the following descriptors would be a suitable set for QSAR analysis? a) logP, molecular volume, Hammet σ and π constants, molar refractivity, polar surface area b) logP, number of synthetic steps, polar surface area, molar refractivity c) logP, number of nitrogen atoms, Hammet σ and π constants, molar refractivity, polar surface area d) molecular weight, molecular volume, molecular surface area. PAM120, PAM80 and PAM60 scoring matrices are most suitable for aligning sequences with a) b) c) d)

40%, 50% and 60% similarity similarit y respectively 60%, 50% and 40% similarity respectively 60%, 40% and 50% similarity similarit y respectively The usefulness of PAM matrices have no relationship with similarities of sequences to be aligned

A protein has three domains domains P, Q, and R, whereas another protein protein has three domains R, S and Q in that order. The preferred alignment algorithm for these two proteins will be a) b) c) d)

Local alignment Global alignment Both algorithms will give the same results None of of the methods are suitable in this case

When p and q are lengths of sequences, the computational complexity of the Needleman and Wunsch algorithm is a) b) c) d)

O(pq) O(p+q) O (q log p) O (pq)



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You are interested in a particular enzyme that is expressed in various human tissues. You have isolated the protein from the brain, liver and kidneys. After a lot of experimentation you determine that the liver protein has three domains A, B and C occurring in sequential order. Domain B is the catalytic domain and the other two have regulatory function. The kidney protein has only domains A and B in that order and the brain protein has domains B and C. You then proceed to determine the primary structure of the proteins using chemical methods and find that the amino acid sequence of the three domains are completely identical regardless of the source from which they were isolated. You then ask the question whether the three different proteins have all originated from the same gene by means of alternative splicing, or they could be products of different genes. Having the experimentally determined protein sequences and knowing the sequence of the human genome, which one of the following bioinformatic method you will use to answer the question above. a) TBLASTN using the protein sequence as query and the human genome sequence as database. b) TBLASTX using the protein sequence as query and the human genome sequence as database. c) BLASTN using the protein sequence as query and the human genome sequence as reference. d) BLASTP using the protein sequence as query and the human genome sequence as reference. Which of the following terms will have to be taken into consideration for developing a potential function for docking simulation? a) b) c) d)

hydrogen bonding, van van der Waal's and electrostati electrostatic c interactio interaction n terms Bond, angle and dihedral terms Dihedral and hydrogen bonding terms Bond, angle and hydrogen bonding terms

References DBT-JRF – Question papers and Answer Keys



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Bioinformatics Quiz: Test Your Knowledge of Bioinformatics

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