Q.1 What is the primary function of bioinformatics?
Analyzing biological data with computers
Building electrical circuits
Studying soil composition
Designing mechanical parts
Explanation - Bioinformatics uses computational tools to analyze and interpret biological data, especially genetic and genomic information.
Correct answer is: Analyzing biological data with computers
Q.2 Which of the following is NOT a type of biological sequence?
DNA
RNA
Protein
Silicon
Explanation - DNA, RNA, and proteins are biological molecules; silicon is a chemical element, not a biological sequence.
Correct answer is: Silicon
Q.3 What does FASTA format represent?
A file format for sequence data
A type of chemical compound
A measurement unit in bioelectricity
An electrical circuit diagram
Explanation - FASTA is a text-based format for representing nucleotide or peptide sequences.
Correct answer is: A file format for sequence data
Q.4 Which tool is commonly used for finding similar sequences in a database?
BLAST
Oscilloscope
Soldering iron
Thermometer
Explanation - BLAST (Basic Local Alignment Search Tool) compares an input sequence against a database to find similar sequences.
Correct answer is: BLAST
Q.5 What does the acronym 'NGS' stand for in genomics?
Next Generation Sequencing
New Gene Sequence
Nuclear Gene Synthesis
Nonlinear Genetic System
Explanation - NGS refers to high-throughput methods that allow rapid sequencing of large amounts of DNA.
Correct answer is: Next Generation Sequencing
Q.6 Which of these is a common source of DNA for sequencing?
Saliva
Water
Air
Oil
Explanation - Saliva contains cells from the mouth, providing a convenient source of DNA.
Correct answer is: Saliva
Q.7 What is a gene?
A unit of heredity made of DNA
A type of electrical component
A piece of plastic used in labs
A software program
Explanation - Genes are sequences of DNA that encode proteins or functional RNA molecules.
Correct answer is: A unit of heredity made of DNA
Q.8 Which software is frequently used for phylogenetic tree construction?
MEGA
Photoshop
Excel
AutoCAD
Explanation - MEGA (Molecular Evolutionary Genetics Analysis) is a program for building phylogenetic trees based on sequence data.
Correct answer is: MEGA
Q.9 In a BLAST search, what does an e-value indicate?
The number of expected matches by chance
The electrical voltage used in sequencing
The length of a DNA fragment
The speed of data transfer
Explanation - An e-value estimates how many alignments one might see by chance; lower values indicate more significant matches.
Correct answer is: The number of expected matches by chance
Q.10 What is a 'motif' in sequence analysis?
A short recurring pattern in DNA or proteins
A type of electrical circuit
A measurement unit
A software license key
Explanation - Motifs are conserved sequences that often have a functional role, like binding sites.
Correct answer is: A short recurring pattern in DNA or proteins
Q.11 Which file format stores raw sequencing reads?
FASTQ
FASTA
PDF
ZIP
Explanation - FASTQ files include sequence data and quality scores for each base, used for raw sequencing outputs.
Correct answer is: FASTQ
Q.12 In bioinformatics, what does 'alignment' refer to?
Arranging sequences to identify similarities
Connecting electrical wires
Setting up lab equipment
Aligning data on a spreadsheet
Explanation - Sequence alignment places nucleotides or amino acids side by side to find homologous regions.
Correct answer is: Arranging sequences to identify similarities
Q.13 What does 'sequence coverage' mean?
The number of times a region is read during sequencing
The depth of a circuit board
The width of a lab bench
The number of files in a folder
Explanation - Coverage indicates how many times a nucleotide is sequenced, affecting confidence in the data.
Correct answer is: The number of times a region is read during sequencing
Q.14 Which algorithm is often used for multiple sequence alignment?
Clustal Omega
BFS
FFT
Dijkstra
Explanation - Clustal Omega is a widely used tool for aligning multiple biological sequences simultaneously.
Correct answer is: Clustal Omega
Q.15 What does a 'gene ontology' (GO) term describe?
A functional annotation of genes
An electrical component's brand
A lab safety procedure
A type of microscope
Explanation - GO terms classify genes based on biological processes, molecular functions, and cellular components.
Correct answer is: A functional annotation of genes
Q.16 Which of the following is a major public database for genetic information?
GenBank
Walmart
Facebook
Google Maps
Explanation - GenBank is a comprehensive public repository of nucleotide sequences maintained by NCBI.
Correct answer is: GenBank
Q.17 What does 'RNA-Seq' measure?
Gene expression levels
DNA mutations
Protein folding rates
Electrical current in cells
Explanation - RNA-Seq sequences RNA to quantify how much each gene is being expressed in a sample.
Correct answer is: Gene expression levels
Q.18 What is a 'phred score' used for?
Indicating base call quality in sequencing
Measuring voltage
Quantifying protein concentration
Rating battery life
Explanation - Phred scores estimate the probability of an incorrect base call; higher scores mean higher confidence.
Correct answer is: Indicating base call quality in sequencing
Q.19 Which term describes a region of DNA that initiates transcription?
Promoter
Enhancer
Silencer
All of the above
Explanation - Promoters are DNA sequences where RNA polymerase binds to start transcription.
Correct answer is: Promoter
Q.20 What is the purpose of a 'masking' step in sequence analysis?
Hide low-complexity or repetitive regions
Apply a protective coating
Block electrical interference
Cover data on a screen
Explanation - Masking removes or flags regions that might produce false positives during alignments.
Correct answer is: Hide low-complexity or repetitive regions
Q.21 Which of these represents a single nucleotide polymorphism (SNP)?
A change of one DNA base in a population
A large chromosomal deletion
A protein folding error
An electrical glitch
Explanation - An SNP is a single base variation at a specific position in the genome.
Correct answer is: A change of one DNA base in a population
Q.22 What does 'exon' refer to in a gene?
A coding region that is spliced into mRNA
A non-coding region
A protein domain
An electrical component
Explanation - Exons are the sequences retained in mature mRNA after intron removal.
Correct answer is: A coding region that is spliced into mRNA
Q.23 Which of the following is a common method to visualize genetic variation?
SNP plot
Bar graph
Pie chart
Line chart
Explanation - SNP plots display the distribution of SNPs across a genome or population.
Correct answer is: SNP plot
Q.24 In bioinformatics, what is a 'phylogenetic tree' used to illustrate?
Evolutionary relationships between species
Electrical circuitry
Chemical reactions
Data flow in networks
Explanation - Phylogenetic trees depict how species are related through common ancestry.
Correct answer is: Evolutionary relationships between species
Q.25 What does 'GC content' refer to?
Percentage of guanine and cytosine in DNA
Amount of gene content
Genomic coverage
General content
Explanation - GC content measures how many G and C nucleotides are present, affecting DNA stability.
Correct answer is: Percentage of guanine and cytosine in DNA
Q.26 Which tool is used for assembling short reads into longer sequences?
SPAdes
Photoshop
Excel
Word
Explanation - SPAdes is a popular genome assembler that constructs longer contigs from short sequencing reads.
Correct answer is: SPAdes
Q.27 What does a 'k-mer' represent?
A substring of k nucleotides
A type of protein
A measurement unit
A data file extension
Explanation - K-mers are all possible subsequences of length k used in many sequence analysis algorithms.
Correct answer is: A substring of k nucleotides
Q.28 Which of these is a typical output of a BLAST search?
Alignment score and e-value
Voltage and current
Temperature reading
Mechanical stress measurement
Explanation - BLAST results include scores indicating similarity and e-values for statistical significance.
Correct answer is: Alignment score and e-value
Q.29 What is the role of an 'alignment score'?
Measures similarity between sequences
Measures electrical resistance
Rates software performance
Quantifies battery life
Explanation - The score quantifies how well two sequences match; higher scores indicate greater similarity.
Correct answer is: Measures similarity between sequences
Q.30 Which of the following databases contains protein structures?
PDB (Protein Data Bank)
GenBank
BLAST
FASTA
Explanation - The Protein Data Bank stores three-dimensional structures of proteins and nucleic acids.
Correct answer is: PDB (Protein Data Bank)
Q.31 What does 'signal peptide' refer to in a protein sequence?
A short amino acid sequence targeting the protein to a location
An electrical signal
A part of a circuit
A type of battery indicator
Explanation - Signal peptides direct proteins to secretory pathways or cellular membranes.
Correct answer is: A short amino acid sequence targeting the protein to a location
Q.32 Which file format is used for representing the quality scores of FASTQ files?
Phred scale
Binary
Text
Image
Explanation - FASTQ quality scores are encoded as Phred scores, indicating confidence in each base call.
Correct answer is: Phred scale
Q.33 What does 'coverage depth' of 30X signify in sequencing?
Each base is read on average 30 times
30 kilobases are sequenced
30 megabases are covered
30% of the genome is sequenced
Explanation - 30X depth means each nucleotide has been read approximately 30 times, improving accuracy.
Correct answer is: Each base is read on average 30 times
Q.34 Which of the following is a commonly used programming language in bioinformatics?
Python
Java
C++
All of the above
Explanation - Python, Java, and C++ are all widely used for writing bioinformatics tools and pipelines.
Correct answer is: All of the above
Q.35 What does 'phylogenetic inference' aim to accomplish?
Reconstruct evolutionary trees
Predict weather patterns
Design electrical circuits
Calculate battery efficiency
Explanation - Phylogenetic inference uses sequence data to deduce the evolutionary relationships among organisms.
Correct answer is: Reconstruct evolutionary trees
Q.36 Which of the following best describes a 'cluster' in genomics?
Group of similar sequences
A type of DNA polymerase
A cluster of cells
An electrical component
Explanation - Clustering groups sequences based on similarity to identify families or functional groups.
Correct answer is: Group of similar sequences
Q.37 What is the main purpose of a 'variant call file (VCF)'?
List genetic variants identified in a sample
Store protein structures
Represent sequence alignment
Archive raw sequencing reads
Explanation - VCF files contain information about SNPs, indels, and other variants detected during sequencing.
Correct answer is: List genetic variants identified in a sample
Q.38 Which of the following is a metric used to assess the quality of a genome assembly?
N50
GC content
e-value
Alignment score
Explanation - N50 is the length such that 50% of the assembled genome is in contigs of that length or longer.
Correct answer is: N50
Q.39 What does 'RNA editing' refer to?
Post-transcriptional changes in RNA sequence
Editing of video files
Modifying electrical signals
Rewriting code
Explanation - RNA editing alters nucleotides after transcription, affecting the final RNA sequence.
Correct answer is: Post-transcriptional changes in RNA sequence
Q.40 Which of the following is NOT a step in a typical bioinformatics workflow?
Data acquisition
Sequence alignment
Circuit design
Statistical analysis
Explanation - Bioinformatics focuses on computational biology; circuit design is unrelated to sequence analysis.
Correct answer is: Circuit design
Q.41 What does the term 'ortholog' mean?
Genes in different species that evolved from a common ancestor
Genes within the same species
A type of electrical connector
An unrelated protein
Explanation - Orthologs are homologous genes in different species that perform similar functions.
Correct answer is: Genes in different species that evolved from a common ancestor
Q.42 Which of the following is a commonly used statistical test for differential expression?
DESeq2
t-test
Chi-squared test
All of the above
Explanation - DESeq2 is a specialized package, but t-tests and chi-squared tests can also be applied depending on data.
Correct answer is: All of the above
Q.43 What is a 'meta-genome'?
The collective genetic material of a microbial community
The genome of a single organism
A synthetic genome
A type of battery
Explanation - Metagenomics studies DNA extracted from environmental samples containing many organisms.
Correct answer is: The collective genetic material of a microbial community
Q.44 Which algorithm is commonly used for de novo genome assembly?
De Bruijn graph
Dijkstra
K-means
Naïve Bayes
Explanation - De Bruijn graphs represent k-mers as nodes and are foundational for assembling short-read data.
Correct answer is: De Bruijn graph
Q.45 What does the term 'copy number variation (CNV)' describe?
Differences in the number of copies of a particular gene
Variations in copywriting rights
Changes in a computer's memory capacity
None of the above
Explanation - CNVs are structural variations where segments of DNA are duplicated or deleted.
Correct answer is: Differences in the number of copies of a particular gene
Q.46 What is a 'protein family'?
A group of proteins with similar sequences or functions
A type of electrical cable
A cluster of cells
An assembly of robots
Explanation - Protein families are classified based on shared motifs and functional similarities.
Correct answer is: A group of proteins with similar sequences or functions
Q.47 Which of the following best describes 'next-generation sequencing' technologies?
High-throughput, massively parallel sequencing methods
Traditional Sanger sequencing
Manual sequencing by hand
Sequencing of mechanical parts
Explanation - NGS platforms allow simultaneous sequencing of millions of fragments, revolutionizing genomics.
Correct answer is: High-throughput, massively parallel sequencing methods
Q.48 In a sequence logo, what does the height of a letter represent?
Information content at that position
Frequency of the nucleotide or amino acid
Statistical significance
Protein mass
Explanation - Sequence logos graphically display conserved positions; taller letters indicate higher conservation.
Correct answer is: Information content at that position
Q.49 What is the purpose of a 'reference genome'?
To serve as a standard for alignment and variant calling
To design electrical circuits
To store chemical recipes
None of the above
Explanation - A reference genome provides a baseline sequence for aligning reads and identifying differences.
Correct answer is: To serve as a standard for alignment and variant calling
Q.50 Which of the following is a commonly used tool for phylogenetic tree visualization?
FigTree
Excel
AutoCAD
Photoshop
Explanation - FigTree is a software application for viewing and editing phylogenetic trees.
Correct answer is: FigTree
Q.51 What does 'reads' refer to in sequencing?
Short DNA fragments obtained from sequencing machines
Printed pages
Electronic signals
Instruction manuals
Explanation - Sequencing reads are the raw DNA or RNA fragments generated during a sequencing run.
Correct answer is: Short DNA fragments obtained from sequencing machines
Q.52 Which type of sequencing provides single-nucleotide resolution?
DNA sequencing
Imaging
Audio recording
Video streaming
Explanation - DNA sequencing methods can determine the exact order of nucleotides in a genome.
Correct answer is: DNA sequencing
Q.53 What does 'heterozygous' mean in genetics?
Having two different alleles at a locus
Having two identical alleles
Having no alleles
Having a single allele
Explanation - Heterozygosity indicates variation in the two copies of a gene.
Correct answer is: Having two different alleles at a locus
Q.54 Which of the following best describes 'in silico' methods?
Computational experiments
Laboratory experiments
Field studies
Astronomical observations
Explanation - In silico refers to experiments performed on a computer or via computational simulations.
Correct answer is: Computational experiments
Q.55 What is a 'promoter' region used for?
To initiate transcription of a gene
To inhibit DNA replication
To cut DNA strands
To label a protein
Explanation - Promoters are DNA sequences recognized by RNA polymerase to start transcription.
Correct answer is: To initiate transcription of a gene
Q.56 Which of these is NOT a typical output from a BLAST run?
Alignment
E-value
Power factor
Score
Explanation - Power factor is an electrical term, not part of BLAST results.
Correct answer is: Power factor
Q.57 In bioinformatics, what does 'annotation' refer to?
Adding functional information to genes or proteins
Painting on a canvas
Marking a battery
Writing code
Explanation - Annotation assigns biological meaning, such as function, to sequences.
Correct answer is: Adding functional information to genes or proteins
Q.58 What is a 'phylogenetic tree' usually represented as?
A branching diagram
A bar chart
A pie chart
A line graph
Explanation - Phylogenetic trees depict evolutionary relationships as branches connecting nodes.
Correct answer is: A branching diagram
Q.59 Which of these tools is used to visualize sequence alignments?
Jalview
AutoCAD
Photoshop
Excel
Explanation - Jalview is a software program for viewing and editing multiple sequence alignments.
Correct answer is: Jalview
Q.60 What is 'gene expression'?
The process by which genes produce proteins or RNAs
The rate of electrical current
The way a circuit is wired
The frequency of a signal
Explanation - Gene expression describes how genetic information is transcribed and translated into functional molecules.
Correct answer is: The process by which genes produce proteins or RNAs
Q.61 Which file format is used to store alignment data in FASTA?
FASTA
FASTQ
PDF
DOCX
Explanation - FASTA is the format for sequences without quality scores; FASTQ includes quality scores.
Correct answer is: FASTA
Q.62 Which of these describes a 'de novo' assembly?
Assembling a genome without a reference
Assembling a genome using a reference
Sequencing a single gene
Translating RNA into protein
Explanation - De novo assembly builds a genome from scratch using overlapping reads.
Correct answer is: Assembling a genome without a reference
Q.63 What is the role of a 'base calling' algorithm?
Determining the nucleotide at each position in a read
Counting electrons
Designing circuits
Calculating voltage
Explanation - Base calling interprets raw signal data to assign DNA bases to each position.
Correct answer is: Determining the nucleotide at each position in a read
Q.64 Which of the following best defines 'mRNA'?
Messenger RNA, the transcript that carries genetic information from DNA to ribosomes
A type of protein
A type of battery
A circuit board
Explanation - mRNA is synthesized from DNA and carries the code to synthesize proteins.
Correct answer is: Messenger RNA, the transcript that carries genetic information from DNA to ribosomes
Q.65 What is a 'tRNA' primarily used for?
Transferring amino acids during translation
Transcribing DNA
Transporting electrons
Binding to a battery terminal
Explanation - tRNA brings specific amino acids to the ribosome according to the codon sequence.
Correct answer is: Transferring amino acids during translation
Q.66 Which of these describes a 'genome browser'?
A tool to visualize and navigate genomic data
A software for editing videos
An electrical measurement device
A type of microscope
Explanation - Genome browsers display genomic features, alignments, and annotations across a reference genome.
Correct answer is: A tool to visualize and navigate genomic data
Q.67 What does 'methylation' refer to in DNA?
The addition of a methyl group to cytosine bases
The removal of bases
The addition of electrons
A type of circuit insulation
Explanation - DNA methylation is an epigenetic modification that can influence gene expression.
Correct answer is: The addition of a methyl group to cytosine bases
Q.68 What is the function of a 'transcription factor'?
Regulating the initiation of transcription
Catalyzing chemical reactions
Acting as a battery
Designing circuits
Explanation - Transcription factors bind DNA and control the rate of gene expression.
Correct answer is: Regulating the initiation of transcription
Q.69 Which of the following is a commonly used format for storing variant data?
VCF
CSV
PDF
DOCX
Explanation - VCF (Variant Call Format) stores information about genetic variants.
Correct answer is: VCF
Q.70 What does a 'phylogenetic tree' illustrate about organisms?
Their evolutionary relationships
Their electrical wiring
Their financial status
Their climate data
Explanation - Phylogenetic trees depict how species are related through common ancestry.
Correct answer is: Their evolutionary relationships
Q.71 What is the main purpose of a 'reference genome' in sequencing projects?
Align reads and identify differences
Store images
Measure voltage
Compute battery life
Explanation - The reference genome serves as a template to which sequencing reads are matched.
Correct answer is: Align reads and identify differences
Q.72 Which of the following is a tool for clustering genes based on expression?
WGCNA
BLAST
Photoshop
AutoCAD
Explanation - WGCNA (Weighted Gene Co-expression Network Analysis) identifies modules of co-expressed genes.
Correct answer is: WGCNA
Q.73 What does a 'heat map' in bioinformatics represent?
Intensity or abundance of data points across a matrix
Temperature distribution in a circuit
Heat signatures in a lab
Color mapping of a city
Explanation - Heat maps display data values (e.g., expression levels) using colors to indicate magnitude.
Correct answer is: Intensity or abundance of data points across a matrix
Q.74 Which of the following best describes 'read mapping'?
Aligning sequencing reads to a reference genome
Drawing a circuit diagram
Creating a timetable
Printing a map
Explanation - Read mapping is the process of assigning sequencing reads to positions on a reference sequence.
Correct answer is: Aligning sequencing reads to a reference genome
Q.75 Which tool is often used for genome annotation?
Prokka
AutoCAD
Photoshop
Excel
Explanation - Prokka is a rapid prokaryotic genome annotation pipeline.
Correct answer is: Prokka
Q.76 What is the 'GC skew' used to identify?
Replication origins and terminus
Signal strength
Voltage drop
Battery capacity
Explanation - GC skew analysis helps locate the start and end points of DNA replication.
Correct answer is: Replication origins and terminus
Q.77 Which of the following is a characteristic of a 'protein secondary structure'?
Alpha helix and beta sheet
Voltage divider
Signal amplifier
Battery terminal
Explanation - Secondary structures refer to regular folding patterns within a polypeptide chain.
Correct answer is: Alpha helix and beta sheet
Q.78 What does 'phylogenetic distance' measure?
Evolutionary divergence between taxa
Physical distance between organisms
Electrical resistance
Signal delay
Explanation - Phylogenetic distance quantifies how far apart species are in evolutionary terms.
Correct answer is: Evolutionary divergence between taxa
Q.79 What is an 'operon'?
A cluster of genes regulated together in prokaryotes
A type of electrical circuit
A group of neurons
A battery pack
Explanation - Operons allow coordinated expression of multiple genes in response to environmental signals.
Correct answer is: A cluster of genes regulated together in prokaryotes
Q.80 Which of the following best describes a 'codon'?
A triplet of nucleotides in mRNA that specifies an amino acid
A circuit component
A type of battery connector
A data packet
Explanation - Codons are three-base sequences that encode the building blocks of proteins.
Correct answer is: A triplet of nucleotides in mRNA that specifies an amino acid
Q.81 Which of these is a commonly used algorithm for multiple sequence alignment?
MAFFT
BFS
FFT
Dijkstra
Explanation - MAFFT is a fast and accurate tool for aligning multiple biological sequences.
Correct answer is: MAFFT
Q.82 What does 'ORF' stand for in genomics?
Open Reading Frame
Operational Reference File
Output Regulatory Factor
Overlapping Recombination Fragment
Explanation - An ORF is a sequence of DNA that could potentially encode a protein.
Correct answer is: Open Reading Frame
Q.83 Which of the following is a feature of a 'balanced sequencing run'?
Even distribution of reads across samples
High noise levels
Low coverage
Uneven amplification
Explanation - Balanced runs allocate similar sequencing depth to each sample for fair comparison.
Correct answer is: Even distribution of reads across samples
Q.84 What does the term 'polyploid' refer to?
Having more than two sets of chromosomes
Having a single chromosome set
Being a polyline graph
Having high voltage
Explanation - Polyploid organisms carry multiple complete sets of chromosomes.
Correct answer is: Having more than two sets of chromosomes
Q.85 Which file format is used for storing protein alignments?
CLUSTAL
FASTA
PDF
DOCX
Explanation - CLUSTAL format stores multiple sequence alignments in a human-readable text file.
Correct answer is: CLUSTAL
Q.86 What is a 'gene regulatory network'?
A system of interactions controlling gene expression
A network of electrical circuits
A social media platform
A traffic system
Explanation - Gene regulatory networks model how genes influence each other's expression through transcription factors and other signals.
Correct answer is: A system of interactions controlling gene expression
Q.87 Which of the following best describes 'protein docking'?
Predicting the binding of two proteins
Fitting a circuit into a case
Mounting a battery
Aligning DNA sequences
Explanation - Protein docking simulates how two proteins interact physically to form complexes.
Correct answer is: Predicting the binding of two proteins
Q.88 Which of these is a measure of how well a genome assembly is contiguous?
N50
GC%
E-value
Alignment score
Explanation - N50 indicates the contig length at which 50% of the genome is represented by contigs of that size or longer.
Correct answer is: N50
Q.89 What is the main difference between 'SNP' and 'INDEL'?
SNP involves a single base change; INDEL involves insertion or deletion of bases
SNP is a type of protein; INDEL is a type of DNA
SNP is in mitochondria; INDEL is in nuclear DNA
They are the same
Explanation - SNPs are single nucleotide substitutions, whereas INDELs involve addition or removal of nucleotides.
Correct answer is: SNP involves a single base change; INDEL involves insertion or deletion of bases
Q.90 What does a 'sequence logo' depict?
The relative frequency of nucleotides or amino acids at each position
The layout of an electrical circuit
The shape of a DNA helix
The color of a protein
Explanation - Sequence logos visually summarize conservation across multiple aligned sequences.
Correct answer is: The relative frequency of nucleotides or amino acids at each position
Q.91 Which of the following is a feature of a 'gene knockout' experiment?
Disruption or deletion of a specific gene to study its function
Overexpressing a gene
Adding a gene copy
Changing a nucleotide in a promoter
Explanation - Knockouts remove gene activity to observe resulting phenotypic changes.
Correct answer is: Disruption or deletion of a specific gene to study its function
Q.92 Which of these is a typical output of a variant calling pipeline?
VCF file
PNG image
PDF report
Excel spreadsheet
Explanation - VCF files store information about identified genetic variants.
Correct answer is: VCF file
Q.93 In RNA-Seq data, what does the term 'FPKM' stand for?
Fragments Per Kilobase of transcript per Million mapped reads
Fold Per Kilobase per Million
Frequency per Kilobase per Minute
Fragments per Kilo per Mole
Explanation - FPKM normalizes read counts by transcript length and sequencing depth.
Correct answer is: Fragments Per Kilobase of transcript per Million mapped reads
Q.94 What does 'metabolomics' study?
Small molecules and metabolites within a biological system
Large DNA sequences
Electrical power consumption
Protein folding
Explanation - Metabolomics examines the chemical fingerprints left by metabolic processes.
Correct answer is: Small molecules and metabolites within a biological system
Q.95 Which of these best describes a 'restriction enzyme'?
An enzyme that cuts DNA at specific sequences
A protein that repairs DNA
An enzyme that synthesizes RNA
A machine that sequences DNA
Explanation - Restriction enzymes recognize specific short sequences and cleave DNA at or near those sites.
Correct answer is: An enzyme that cuts DNA at specific sequences
Q.96 What is the main purpose of a 'blastp' search?
Searching a protein database for similar sequences
Searching a nucleotide database
Sequencing DNA directly
Analyzing electrical circuits
Explanation - blastp compares an input protein sequence against a protein database.
Correct answer is: Searching a protein database for similar sequences
Q.97 What does 'phylogenomics' integrate?
Genomic data and phylogenetics
Electrical engineering and biology
Chemistry and physics
Art and design
Explanation - Phylogenomics uses whole-genome data to infer evolutionary relationships.
Correct answer is: Genomic data and phylogenetics
Q.98 Which of the following is a common format for representing gene annotations in GFF?
GFF3
FASTA
VCF
FASTQ
Explanation - GFF3 (General Feature Format) stores information about genomic features such as genes and exons.
Correct answer is: GFF3
Q.99 What is a 'bioinformatics pipeline'?
A sequence of automated computational steps to analyze data
A type of pipeline in plumbing
A sequence of electrical components
A biological laboratory setup
Explanation - Pipelines streamline data processing, from raw reads to final results.
Correct answer is: A sequence of automated computational steps to analyze data
Q.100 Which of these best describes 'snp calling'?
Identifying single nucleotide variants from sequencing data
Finding protein structures
Building a phylogenetic tree
Designing an electronic circuit
Explanation - SNP calling analyzes sequencing reads to detect positions with variation.
Correct answer is: Identifying single nucleotide variants from sequencing data
Q.101 Which file extension is associated with a FASTQ file?
.fastq
.txt
.docx
.jpg
Explanation - FASTQ files end with .fastq and contain sequence and quality information.
Correct answer is: .fastq
Q.102 What is the role of a 'karyotype' in genetics?
Visual representation of chromosomes in an organism
An electrical schematic
A type of battery
A DNA sequencing method
Explanation - Karyotypes display chromosome number, shape, and size for genetic analysis.
Correct answer is: Visual representation of chromosomes in an organism
Q.103 Which of these best describes a 'metagenomic assembly'?
Assembling sequences from a mixed microbial community
Assembling a single organism's genome
Sequencing a single gene
Transcribing RNA to protein
Explanation - Metagenomic assemblies reconstruct genomes from environmental samples containing many species.
Correct answer is: Assembling sequences from a mixed microbial community
Q.104 What does 'gene ontology' provide?
Standardized vocabulary for gene functions
Voltage ratings for circuits
Battery efficiency metrics
Data compression algorithms
Explanation - Gene Ontology organizes gene functions into three categories: biological process, cellular component, and molecular function.
Correct answer is: Standardized vocabulary for gene functions
Q.105 Which of the following is a typical step in preparing data for a machine learning model in bioinformatics?
Feature extraction from sequences
Soldering components
Drawing circuit diagrams
Calibrating a thermometer
Explanation - Extracting meaningful features from biological data is essential before feeding them into machine learning algorithms.
Correct answer is: Feature extraction from sequences
Q.106 Which of these best describes a 'gene fusion' event?
Combining parts of two genes into a single transcript
Merging two circuits into one
Joining two batteries
Linking two proteins chemically
Explanation - Gene fusions create chimeric proteins that can have altered functions or be oncogenic.
Correct answer is: Combining parts of two genes into a single transcript
Q.107 What does a 'phred quality score' of 30 mean?
0.1% chance of error in the base call
0.01% chance of error
10% chance of error
100% confidence
Explanation - Phred scores are calculated as -10 log10(P(error)); a score of 30 corresponds to a 1 in 1000 error rate.
Correct answer is: 0.1% chance of error in the base call
Q.108 Which of the following is a function of the 'spliced leader' in some eukaryotes?
Adding a short sequence to the 5' end of all mRNAs
Adding a barcode to DNA fragments
Attaching a protein to a membrane
Securing a circuit board
Explanation - The spliced leader is a common leader sequence added during trans-splicing in some organisms.
Correct answer is: Adding a short sequence to the 5' end of all mRNAs
Q.109 What is the main output of a 'de novo transcriptome assembly'?
Reconstructed mRNA sequences
Protein structures
Genomic DNA sequences
Metabolite profiles
Explanation - Transcriptome assembly reconstructs full-length transcripts from short RNA-Seq reads.
Correct answer is: Reconstructed mRNA sequences
Q.110 Which of the following is NOT a common step in variant filtering?
Removing low-quality calls
Excluding common SNPs
Adding random noise
Applying population frequency thresholds
Explanation - Variant filtering aims to improve accuracy, not introduce randomness.
Correct answer is: Adding random noise
Q.111 What does 'BUSCO' assess in a genome assembly?
Completeness based on conserved orthologs
Voltage stability
Battery health
Protein folding accuracy
Explanation - BUSCO checks for presence of universal single-copy orthologs to gauge assembly completeness.
Correct answer is: Completeness based on conserved orthologs
Q.112 Which of these best describes 'epistasis'?
Interaction between genes that influence phenotypic expression
Electrical interference between circuits
Chemical reaction between metabolites
Signal amplification in a circuit
Explanation - Epistasis refers to genetic interactions where one gene modifies the effect of another.
Correct answer is: Interaction between genes that influence phenotypic expression
Q.113 What is the purpose of a 'feature table' in genome annotation?
Listing genomic features and their coordinates
Listing circuit components
Listing battery specifications
Listing data packet sizes
Explanation - Feature tables specify locations of genes, exons, and other genomic elements.
Correct answer is: Listing genomic features and their coordinates
Q.114 Which of these tools is used to visualize large phylogenies?
iTOL (Interactive Tree Of Life)
AutoCAD
Photoshop
Excel
Explanation - iTOL is a web-based tool for interactive visualization of phylogenetic trees.
Correct answer is: iTOL (Interactive Tree Of Life)
Q.115 What does 'HMM' stand for in bioinformatics?
Hidden Markov Model
High Memory Machine
Homozygous Mutation Method
Hierarchical Matrix Method
Explanation - HMMs are probabilistic models used for sequence analysis, e.g., gene prediction.
Correct answer is: Hidden Markov Model
Q.116 Which of the following best describes a 'genome browser'?
A web-based interface to visualize genomic data
A physical browser for books
A type of circuit board
A chemical reagent
Explanation - Genome browsers provide interactive exploration of genomic annotations and alignments.
Correct answer is: A web-based interface to visualize genomic data
Q.117 Which of these best defines 'orthogonal' in a bioinformatics context?
Two variables that are independent of each other
Two circuits that interfere
Two proteins that bind each other
Two battery terminals that are identical
Explanation - Orthogonal variables do not influence each other, often used in statistical analyses.
Correct answer is: Two variables that are independent of each other
Q.118 What is the main role of a 'read trimming' tool?
Removing low-quality bases and adapter sequences from reads
Adding adapters to reads
Aligning reads to a reference
Visualizing reads
Explanation - Trimming improves downstream analyses by eliminating unreliable data.
Correct answer is: Removing low-quality bases and adapter sequences from reads
Q.119 Which of the following is an example of a 'gene set enrichment analysis'?
Identifying overrepresented pathways in a list of differentially expressed genes
Identifying electrical circuits in a chip
Mapping the battery life of devices
Determining the color of a protein gel
Explanation - GSEA tests whether a predefined gene set shows statistically significant differences between two phenotypes.
Correct answer is: Identifying overrepresented pathways in a list of differentially expressed genes
Q.120 What does 'UMI' stand for in next-generation sequencing?
Unique Molecular Identifier
Ultra-Mega-Index
Universal Mapping Input
User-Managed Interface
Explanation - UMIs are short sequences added to each DNA fragment to identify duplicates and reduce bias.
Correct answer is: Unique Molecular Identifier
Q.121 What is the main output of a 'proteogenomics' approach?
Integration of proteomic and genomic data to improve gene models
A new type of circuit
A battery with higher efficiency
A chemical reaction scheme
Explanation - Proteogenomics uses mass spectrometry data to refine gene predictions and annotate novel proteins.
Correct answer is: Integration of proteomic and genomic data to improve gene models
Q.122 Which of these best describes 'genome-wide association study (GWAS)'?
Scanning the genome for variants associated with a trait
Sequencing the entire genome of one individual
Mapping electrical circuits
Testing battery performance across a population
Explanation - GWAS correlates genetic variants across many individuals with phenotypic traits or diseases.
Correct answer is: Scanning the genome for variants associated with a trait
Q.123 Which of the following is a common method for visualizing differential gene expression?
Volcano plot
Line graph
Bar chart
Pie chart
Explanation - A volcano plot displays statistical significance versus fold-change for each gene.
Correct answer is: Volcano plot
Q.124 What does 'phylogenetic bootstrap' assess?
Support for branches in a phylogenetic tree
Voltage stability of a circuit
Signal noise in an amplifier
Battery life under load
Explanation - Bootstrapping resamples data to estimate confidence levels for tree branches.
Correct answer is: Support for branches in a phylogenetic tree
Q.125 Which of the following best describes 'transposon' activity?
Movement of DNA elements within the genome
Movement of a battery in a circuit
Transmission of electrical signals
Transport of metabolites
Explanation - Transposons can copy or cut-and-paste themselves, impacting genome structure.
Correct answer is: Movement of DNA elements within the genome
Q.126 What is the purpose of a 'gene ontology (GO) enrichment' analysis?
To determine which GO terms are overrepresented in a gene list
To calculate battery efficiency
To design an electrical circuit
To map protein structures
Explanation - GO enrichment highlights biological processes or functions that are statistically enriched.
Correct answer is: To determine which GO terms are overrepresented in a gene list
Q.127 Which of the following is a key metric in evaluating RNA-Seq differential expression?
False discovery rate (FDR)
Voltage drop
Battery capacity
Signal delay
Explanation - FDR controls the expected proportion of false positives among significant findings.
Correct answer is: False discovery rate (FDR)
Q.128 What does 'k-mer spectrum' analysis help identify?
Repeats and genome size estimates
Circuit impedance
Battery voltage
Protein folding patterns
Explanation - K-mer frequencies can reveal genome characteristics such as size, heterozygosity, and repeats.
Correct answer is: Repeats and genome size estimates
Q.129 Which of these best defines 'metatranscriptomics'?
Sequencing RNA from environmental samples to study community gene expression
Sequencing DNA from a single organism
Studying protein structures
Analyzing electrical signals in circuits
Explanation - Metatranscriptomics captures the active transcriptome of microbial communities.
Correct answer is: Sequencing RNA from environmental samples to study community gene expression
Q.130 What is the main advantage of using a 'paired-end' sequencing approach?
Improved accuracy and ability to resolve repeats
Lower cost
Longer reads
Single-read coverage
Explanation - Paired-end reads provide two reads from opposite ends of a fragment, aiding assembly and alignment.
Correct answer is: Improved accuracy and ability to resolve repeats
Q.131 Which of these tools is commonly used for de novo transcriptome assembly?
Trinity
BLAST
Photoshop
AutoCAD
Explanation - Trinity reconstructs full-length transcripts from short-read RNA-Seq data.
Correct answer is: Trinity
Q.132 In phylogenetics, what does the 'likelihood ratio test' compare?
Two different tree models
Two different electrical circuits
Two chemical reactions
Two battery chemistries
Explanation - The likelihood ratio test evaluates which evolutionary model better explains the data.
Correct answer is: Two different tree models
Q.133 Which of the following is NOT a standard format for storing sequencing quality scores?
Phred+33
Phred+64
Phred+22
Phred+0
Explanation - Standard Phred encodings start at +33 or +64; +22 and +0 are not standard.
Correct answer is: Phred+0
Q.134 What does 'RNA-Seq coverage' refer to?
The average number of reads mapping to each base of a transcript
The depth of DNA sequencing
The voltage across a circuit
The battery life of a device
Explanation - Coverage indicates how thoroughly a transcript is represented in the sequencing data.
Correct answer is: The average number of reads mapping to each base of a transcript
Q.135 Which of these best describes a 'circular genome'?
Genome with no linear ends, common in bacteria and mitochondria
Genome that is looped in a circuit
A type of battery
A protein structure
Explanation - Circular genomes are closed loops of DNA, lacking termini.
Correct answer is: Genome with no linear ends, common in bacteria and mitochondria
Q.136 What is a 'chromosome painting' in cytogenetics?
Using fluorescent probes to label specific chromosomal regions
Painting a chromosome with paint
Mapping electrical circuits onto a chromosome
Annotating protein sequences
Explanation - Chromosome painting visualizes chromosomal segments in different colors via FISH techniques.
Correct answer is: Using fluorescent probes to label specific chromosomal regions
Q.137 Which of the following is a type of 'RNA modification' that affects translation?
N6-methyladenosine (m6A)
Phosphorus addition
Soldering
Battery charging
Explanation - m6A is a common RNA modification influencing stability and translation efficiency.
Correct answer is: N6-methyladenosine (m6A)
Q.138 Which of the following best describes a 'phylogenetic tree reconciliation'?
Aligning gene trees with species trees to infer duplication or loss events
Rewiring electrical circuits
Recharging a battery
Reassembling a genome
Explanation - Reconciliation identifies evolutionary events like duplications, losses, or horizontal transfers.
Correct answer is: Aligning gene trees with species trees to infer duplication or loss events
Q.139 What is the purpose of a 'genome annotation pipeline' like MAKER?
Automating gene prediction and annotation across multiple genomes
Designing electrical boards
Creating battery safety protocols
Drawing electrical diagrams
Explanation - MAKER integrates evidence-based gene predictions with annotation tools.
Correct answer is: Automating gene prediction and annotation across multiple genomes
Q.140 Which of these is a key component of a 'genome assembly graph'?
Nodes representing k-mers and edges representing overlaps
Vertices representing circuits
Edges representing battery connections
Nodes representing chemical compounds
Explanation - Assembly graphs depict how k-mers connect during de novo assembly.
Correct answer is: Nodes representing k-mers and edges representing overlaps
Q.141 Which of these best defines 'gene fusion proteins'?
Proteins that contain domains from two distinct ancestral proteins
Proteins that fuse with DNA
Proteins that fuse with RNA
Proteins that fuse with circuits
Explanation - Gene fusions create chimeric proteins, often seen in cancer and evolution.
Correct answer is: Proteins that contain domains from two distinct ancestral proteins
Q.142 In a phylogenetic analysis, what is meant by a 'long branch attraction' artifact?
Incorrect grouping of distantly related taxa due to high substitution rates
Electrical interference in a circuit
Anomaly in battery performance
Mislabeling of data files
Explanation - Long branch attraction can lead to misplacement of rapidly evolving lineages in a tree.
Correct answer is: Incorrect grouping of distantly related taxa due to high substitution rates
Q.143 What does a 'phylogenetic footprinting' technique aim to identify?
Conserved regulatory elements across species
Circuit footprints in a PCB
Battery wear patterns
Protein folding motifs
Explanation - Phylogenetic footprinting finds conserved non-coding sequences that likely serve regulatory roles.
Correct answer is: Conserved regulatory elements across species
Q.144 Which of these describes a 'variant allele frequency' in a population?
The proportion of individuals carrying a particular allele
The voltage of a circuit element
The brightness of an LED
The charge capacity of a battery
Explanation - Allele frequency quantifies how common an allele is in a population sample.
Correct answer is: The proportion of individuals carrying a particular allele
Q.145 Which of the following best characterizes a 'protein-protein interaction (PPI) network'?
A graph where nodes are proteins and edges represent interactions
A circuit diagram
A battery connection scheme
A DNA sequence alignment
Explanation - PPIs illustrate how proteins function together in cellular processes.
Correct answer is: A graph where nodes are proteins and edges represent interactions
Q.146 What is the purpose of a 'multiple sequence alignment (MSA)' in evolutionary studies?
Identifying conserved residues and inferring evolutionary relationships
Designing a circuit board layout
Measuring battery efficiency
Predicting weather patterns
Explanation - MSAs highlight shared positions that can be used to build phylogenies.
Correct answer is: Identifying conserved residues and inferring evolutionary relationships
Q.147 Which of these best defines a 'genome browser track'?
A layer of information (e.g., gene annotations, read depth) displayed in a genome browser
A track in a sports race
A circuit track in a PCB
An audio track on a CD
Explanation - Tracks allow users to visualize different data types side by side over a reference genome.
Correct answer is: A layer of information (e.g., gene annotations, read depth) displayed in a genome browser
Q.148 Which of these best describes a 'genome-wide scan for selection'?
Identifying genomic regions under selective pressure by detecting unusual patterns of variation
Scanning for electrical faults
Testing battery life
Scanning a circuit board for defects
Explanation - Selection scans use statistical methods to detect regions with reduced genetic diversity or high differentiation.
Correct answer is: Identifying genomic regions under selective pressure by detecting unusual patterns of variation
Q.149 Which of the following is a characteristic of a 'coding sequence (CDS)'?
A DNA segment that encodes a protein
A non-coding region
A chemical reagent
An electrical component
Explanation - The coding sequence contains codons that are translated into amino acids.
Correct answer is: A DNA segment that encodes a protein
Q.150 Which of these best describes 'linkage disequilibrium (LD)'?
Non-random association of alleles at different loci in a population
Electrical interference between components
Chemical reaction between metabolites
Signal distortion in an amplifier
Explanation - LD measures how often alleles are inherited together more or less often than expected by chance.
Correct answer is: Non-random association of alleles at different loci in a population
Q.151 What is the main function of an 'ORF finder' tool?
Identifying potential protein-coding regions in a sequence
Finding circuit orphans
Locating battery terminals
Scanning for signal peaks
Explanation - ORF finders predict where proteins may start and end based on start/stop codons.
Correct answer is: Identifying potential protein-coding regions in a sequence
Q.152 Which of the following is a common output of a 'gene prediction' software like Augustus?
Predicted gene coordinates and exon-intron structure
Circuit diagrams
Battery specifications
Signal waveforms
Explanation - Gene prediction tools annotate coding regions within a genome sequence.
Correct answer is: Predicted gene coordinates and exon-intron structure
Q.153 In a 'genome assembly', what is a 'contig'?
A contiguous sequence assembled from overlapping reads
A circuit component
A battery cell
A protein domain
Explanation - Contigs are the continuous stretches of DNA constructed during assembly.
Correct answer is: A contiguous sequence assembled from overlapping reads
Q.154 Which of the following best describes the 'coverage threshold' in a variant calling pipeline?
The minimum read depth required for a variant to be considered reliable
The maximum voltage in a circuit
The maximum battery capacity
The maximum data transfer rate
Explanation - Setting a coverage threshold helps filter out low-confidence variant calls.
Correct answer is: The minimum read depth required for a variant to be considered reliable
Q.155 What does the term 'RNA velocity' estimate?
The direction and speed of gene expression changes over time
The speed of electrons in a circuit
The rate of battery discharge
The tempo of a musical piece
Explanation - RNA velocity infers future transcriptional states based on spliced and unspliced RNA ratios.
Correct answer is: The direction and speed of gene expression changes over time
Q.156 Which of these is an example of a 'transcription factor binding site' motif?
TATA box
Capacitance
Resistor value
LED color
Explanation - The TATA box is a common promoter motif recognized by transcription machinery.
Correct answer is: TATA box
Q.157 What is a 'functional annotation pipeline' primarily used for?
Assigning biological functions to genes or proteins
Designing electronic schematics
Specifying battery chemistry
Mapping electrical currents
Explanation - Such pipelines integrate various evidence sources to predict gene function.
Correct answer is: Assigning biological functions to genes or proteins
Q.158 Which of these best defines 'gene duplication'?
The process by which a gene is copied within a genome, creating paralogs
The deletion of a gene
The repair of a DNA strand
The synthesis of a new circuit
Explanation - Gene duplication provides material for evolutionary innovation.
Correct answer is: The process by which a gene is copied within a genome, creating paralogs
Q.159 What is the main purpose of an 'alignment file' in SAM/BAM format?
Storing read alignments to a reference genome
Storing circuit schematics
Storing battery specifications
Storing protein structures
Explanation - SAM/BAM files record where each sequencing read aligns relative to the reference.
Correct answer is: Storing read alignments to a reference genome
Q.160 Which of these tools is used for visualizing genomic variant data in a browser?
IGV (Integrative Genomics Viewer)
AutoCAD
Photoshop
Excel
Explanation - IGV allows interactive exploration of sequence alignments, variants, and annotations.
Correct answer is: IGV (Integrative Genomics Viewer)
Q.161 What does 'phasing' of genetic variants refer to?
Determining which variants are on the same chromosome copy
Measuring electrical phase in circuits
Determining battery charge phase
Sequencing the first half of a genome
Explanation - Phasing resolves haplotypes by assigning variants to maternal or paternal chromosomes.
Correct answer is: Determining which variants are on the same chromosome copy
Q.162 Which of the following is a measure of 'genomic divergence' between two species?
Percentage of nucleotide differences
Voltage difference
Battery capacity difference
Signal amplitude difference
Explanation - Genomic divergence is quantified by comparing sequence differences across species.
Correct answer is: Percentage of nucleotide differences
Q.163 What is the purpose of a 'gene set enrichment analysis (GSEA)' in transcriptomics?
Determining whether predefined gene sets show statistically significant differences between two biological states
Analyzing circuit diagrams
Measuring battery life
Identifying protein folding patterns
Explanation - GSEA ranks all genes and tests enrichment of known gene sets at the extremes of the list.
Correct answer is: Determining whether predefined gene sets show statistically significant differences between two biological states
Q.164 What does the 'genetic code' define?
Mapping of codons to amino acids
Voltage levels in a circuit
Chemical reaction rates
Battery chemistry
Explanation - The genetic code specifies which amino acid each three-base codon encodes.
Correct answer is: Mapping of codons to amino acids
Q.165 Which of these best describes 'alternative splicing'?
Generating multiple mRNA variants from a single gene by including or excluding exons
Changing the color of a LED
Rearranging a circuit board
Mixing batteries for higher voltage
Explanation - Alternative splicing produces diverse proteins from a single gene.
Correct answer is: Generating multiple mRNA variants from a single gene by including or excluding exons
Q.166 What is a 'biological pathway' in the context of pathway analysis?
A series of biochemical reactions leading to a specific product
A series of steps in an electrical circuit
A series of steps in battery charging
A series of steps in data transfer
Explanation - Pathways describe how molecules interact within cells to produce metabolic or signaling outcomes.
Correct answer is: A series of biochemical reactions leading to a specific product
Q.167 Which of these best describes a 'protein domain'?
A conserved structural and functional unit within a protein
A region of a circuit that resists current
A section of a battery cell
An area of a gene with no function
Explanation - Protein domains are independent folding units that can perform distinct functions.
Correct answer is: A conserved structural and functional unit within a protein
Q.168 What is 'gene co-expression network' used for?
Identifying groups of genes that exhibit similar expression patterns
Designing a circuit with synchronized components
Measuring battery discharge curves
Mapping signal propagation in an amplifier
Explanation - Co-expression networks cluster genes with correlated expression, suggesting shared regulation.
Correct answer is: Identifying groups of genes that exhibit similar expression patterns
Q.169 Which of these best describes 'DNA replication origin'?
A specific sequence where DNA replication initiates in a cell
A spot where a circuit begins
A starting point for battery charging
A point in an electrical signal waveform
Explanation - Replication origins are key sites for the assembly of the replication machinery.
Correct answer is: A specific sequence where DNA replication initiates in a cell
Q.170 What does the 'transcriptome' comprise?
All RNA molecules expressed in a cell or tissue
All proteins in a cell
All DNA molecules in a cell
All electrical currents in a circuit
Explanation - The transcriptome represents the complete set of transcripts present under specific conditions.
Correct answer is: All RNA molecules expressed in a cell or tissue
Q.171 Which of these best describes 'functional genomics'?
Studying the functions of genes and gene products at a genome-wide scale
Designing electrical functions in circuits
Measuring battery capacity
Analyzing signal processing
Explanation - Functional genomics seeks to link genotype to phenotype across the genome.
Correct answer is: Studying the functions of genes and gene products at a genome-wide scale