Q.1 Which bioinformatics tool is most commonly used to align multiple DNA sequences to identify conserved regions in crop genomes?
BLAST
ClustalW
FASTA
MEGA
Explanation - ClustalW performs multiple sequence alignment, allowing researchers to detect conserved motifs across many sequences, which is essential for marker discovery in crops.
Correct answer is: ClustalW
Q.2 What is the primary purpose of marker‑assisted selection (MAS) in plant breeding?
To increase the size of the genome
To speed up the identification of desirable traits using DNA markers
To replace all traditional breeding methods
To edit the genome directly
Explanation - MAS uses DNA markers linked to traits of interest, enabling breeders to select plants carrying those traits without waiting for phenotypic expression.
Correct answer is: To speed up the identification of desirable traits using DNA markers
Q.3 Which database provides curated information on plant genomes, including gene models and functional annotation?
NCBI RefSeq
EnsemblPlants
Protein Data Bank
GenBank
Explanation - EnsemblPlants is a specialized portal that aggregates genome assemblies, gene predictions, and functional annotation for many plant species.
Correct answer is: EnsemblPlants
Q.4 In metagenomic analysis of fermented food, which step converts raw sequencing reads into taxonomic profiles?
Genome assembly
Read trimming
Operational Taxonomic Unit (OTU) clustering
Gene prediction
Explanation - OTU clustering groups similar reads and assigns them to known taxonomic units, providing a snapshot of microbial community composition.
Correct answer is: Operational Taxonomic Unit (OTU) clustering
Q.5 Which of the following is a common application of CRISPR‑Cas9 guided by bioinformatic target design in agriculture?
Increasing the speed of DNA sequencing
Predicting soil moisture levels
Knocking out genes that confer susceptibility to disease
Measuring chlorophyll fluorescence
Explanation - Bioinformatics identifies target sequences for CRISPR, allowing precise gene knockout to improve disease resistance in crops.
Correct answer is: Knocking out genes that confer susceptibility to disease
Q.6 What does the term ‘SNP’ stand for, and why are SNPs important in food biotechnology?
Standard Nucleotide Pattern; used for DNA replication
Single Nucleotide Polymorphism; markers for trait selection
Simple Nucleotide Protein; involved in protein synthesis
Sequenced Nucleic Prototype; used for genome assembly
Explanation - SNPs are single‑base variations that can be linked to desirable agronomic traits, making them powerful markers in breeding programs.
Correct answer is: Single Nucleotide Polymorphism; markers for trait selection
Q.7 Which computational method is used to predict potential allergenic proteins in novel food products?
Phylogenetic tree reconstruction
Homology‑based allergenicity prediction (e.g., using AllergenOnline)
Gene expression profiling
Metabolite flux analysis
Explanation - Allergenicity prediction compares protein sequences against known allergens to flag potential cross‑reactivity.
Correct answer is: Homology‑based allergenicity prediction (e.g., using AllergenOnline)
Q.8 In the context of precision agriculture, what role does bioinformatics play when integrating data from IoT soil sensors?
It directly controls irrigation valves
It analyzes genomic data of soil microbes to recommend fertilizer regimes
It visualizes weather forecasts
It predicts market prices for crops
Explanation - Bioinformatics can process metagenomic data from soil sensors to determine microbial community health, guiding nutrient management.
Correct answer is: It analyzes genomic data of soil microbes to recommend fertilizer regimes
Q.9 Which software platform provides a web‑based environment for building reproducible bioinformatics pipelines in agriculture?
MATLAB
Galaxy
AutoCAD
SolidWorks
Explanation - Galaxy offers a user‑friendly, web‑based interface for constructing and sharing reproducible analysis workflows, widely used in plant genomics.
Correct answer is: Galaxy
Q.10 A farmer wants to select wheat varieties with drought tolerance. Which type of omics data is most informative for this purpose?
Proteomics of seed proteins
Transcriptomics of roots under water‑stress
Metabolomics of leaf pigments
Lipidomics of grain oil
Explanation - Root transcriptome profiling under drought reveals genes that regulate water uptake and stress response, aiding selection of tolerant varieties.
Correct answer is: Transcriptomics of roots under water‑stress
Q.11 Which statistical model is commonly used in genomic selection to predict breeding values from high‑density SNP data?
Linear regression
Random forest
Best Linear Unbiased Prediction (BLUP)
K‑means clustering
Explanation - Genomic BLUP incorporates SNP effects into a mixed model to estimate the genetic merit of individuals.
Correct answer is: Best Linear Unbiased Prediction (BLUP)
Q.12 What is the main advantage of using a reference‑free (de‑novo) assembly approach for a newly discovered fruit species?
It requires less computational power
It avoids bias caused by using a distant reference genome
It automatically annotates all genes
It provides immediate functional predictions
Explanation - De‑novo assembly constructs the genome from scratch, preventing errors that arise when aligning reads to an unrelated reference.
Correct answer is: It avoids bias caused by using a distant reference genome
Q.13 Which of the following best describes a ‘pan‑genome’ in crop research?
The genome of a single elite cultivar
The sum of core and dispensable genes across multiple varieties
A synthetic genome created in the lab
Only the mitochondrial DNA of plants
Explanation - A pan‑genome captures all genetic variation present in a species, including genes shared by all members (core) and those unique to some (dispensable).
Correct answer is: The sum of core and dispensable genes across multiple varieties
Q.14 When analyzing the nutritional quality of a novel grain, which bioinformatics resource helps predict the amino‑acid composition of its proteins?
KEGG PATHWAY
UniProtKB/Swiss‑Prot
Pfam
InterPro
Explanation - UniProt provides curated protein sequences with detailed annotations, including amino‑acid composition and functional properties.
Correct answer is: UniProtKB/Swiss‑Prot
Q.15 Which type of machine‑learning algorithm is most frequently applied to classify disease‑causing pathogens in raw sequencing data from food samples?
Support Vector Machine (SVM)
Convolutional Neural Network (CNN)
Decision Tree
Naïve Bayes
Explanation - SVMs handle high‑dimensional genomic data well and have been successfully used for pathogen classification in metagenomic datasets.
Correct answer is: Support Vector Machine (SVM)
Q.16 What is the purpose of a ‘gene ontology’ (GO) term in functional annotation of plant genomes?
To indicate the chromosome number of a gene
To describe the gene’s location on the map
To categorize the gene’s molecular function, biological process, and cellular component
To provide the gene’s DNA melting temperature
Explanation - GO terms provide standardized descriptors of gene products, facilitating comparative analyses across species.
Correct answer is: To categorize the gene’s molecular function, biological process, and cellular component
Q.17 Which technique combines high‑throughput sequencing with computational analysis to study the expression of all genes in a plant under salt stress?
RNA‑Seq
ChIP‑Seq
ATAC‑Seq
SNP genotyping
Explanation - RNA‑Seq quantifies transcript levels genome‑wide, revealing which genes are up‑ or down‑regulated during salt stress.
Correct answer is: RNA‑Seq
Q.18 In the context of food safety, which bioinformatic approach can quickly detect the presence of antibiotic‑resistance genes in a bacterial isolate from milk?
Phylogenetic tree construction
Resistome profiling using tools like ARG‑ANNOT
Metabolic pathway reconstruction
Promoter motif analysis
Explanation - Resistome tools scan genomic sequences for known resistance determinants, providing rapid risk assessment for food products.
Correct answer is: Resistome profiling using tools like ARG‑ANNOT
Q.19 Which data format is standard for storing raw sequencing reads before quality control?
FASTA
BED
FASTQ
GFF
Explanation - FASTQ files contain both the nucleotide sequences and corresponding quality scores for each read.
Correct answer is: FASTQ
Q.20 A researcher wants to predict the three‑dimensional structure of an enzyme involved in starch breakdown. Which bioinformatics tool would be most appropriate?
BLAST
ClustalW
AlphaFold
Bowtie
Explanation - AlphaFold uses deep learning to predict protein 3D structures from amino‑acid sequences with high accuracy.
Correct answer is: AlphaFold
Q.21 Which of the following is a key advantage of using whole‑genome resequencing over SNP arrays for crop improvement?
Lower cost per sample
Higher density of variant detection, including rare alleles
Simpler data analysis
Requires no bioinformatics expertise
Explanation - Whole‑genome resequencing captures all variants, providing a more comprehensive view of genetic diversity than predefined SNP arrays.
Correct answer is: Higher density of variant detection, including rare alleles
Q.22 Which pathway database is frequently used to map metabolic routes of bioactive compounds in fruits?
Reactome
KEGG
STRING
Pfam
Explanation - KEGG links genes and enzymes to metabolic pathways, allowing visualization of biosynthetic routes for phytochemicals.
Correct answer is: KEGG
Q.23 What does the term ‘linkage disequilibrium’ (LD) refer to in plant genetics?
The physical distance between two genes on a chromosome
The non‑random association of alleles at different loci
The rate at which DNA mutates
The expression level of a gene under stress
Explanation - LD measures how often specific allele combinations are inherited together, informing marker selection for breeding.
Correct answer is: The non‑random association of alleles at different loci
Q.24 Which of the following bioinformatics pipelines would be most suitable for assembling the chloroplast genome of a newly sequenced tomato variety?
SPAdes followed by Pilon polishing
Bowtie2 alignment to a reference genome
MAFFT multiple sequence alignment
GATK variant calling
Explanation - SPAdes excels at de‑novo assembly of small genomes; Pilon corrects errors using read data, yielding a high‑quality chloroplast assembly.
Correct answer is: SPAdes followed by Pilon polishing
Q.25 In the context of bioinformatics for agriculture, what is a ‘genomic selection index’ used for?
Measuring soil pH
Ranking individuals based on predicted genetic merit for multiple traits
Calculating the energy content of grains
Determining the optimum planting date
Explanation - The index combines marker effects across the genome to estimate overall breeding value, accelerating selection decisions.
Correct answer is: Ranking individuals based on predicted genetic merit for multiple traits
Q.26 Which sequencing technology is known for producing very long reads, facilitating the resolution of repetitive regions in plant genomes?
Illumina short‑read sequencing
Sanger sequencing
Oxford Nanopore Technologies
Roche 454
Explanation - Nanopore sequencing can generate reads exceeding tens of kilobases, helping assemble complex plant genomes with repeats.
Correct answer is: Oxford Nanopore Technologies
Q.27 A bioinformatician is interested in the evolutionary relationship among different rice cultivars. Which method should they use?
Differential gene expression analysis
Phylogenetic tree construction using maximum likelihood
Gene ontology enrichment
Metabolite profiling
Explanation - Maximum‑likelihood phylogenies estimate evolutionary distances based on sequence data, revealing relationships among cultivars.
Correct answer is: Phylogenetic tree construction using maximum likelihood
Q.28 What is the main output of a genome‑wide association study (GWAS) in crop research?
A list of environmental factors affecting growth
Chromosome maps showing loci associated with a trait
Protein 3‑D structures
Metabolic flux rates
Explanation - GWAS identifies statistical associations between genetic markers and phenotypic traits, producing a map of significant loci.
Correct answer is: Chromosome maps showing loci associated with a trait
Q.29 Which of the following best describes the role of ‘transcript isoform analysis’ in improving fruit flavor?
Identifying DNA methylation patterns
Quantifying different splice variants of flavor‑related genes
Measuring soil nutrient levels
Predicting fruit weight
Explanation - Different isoforms can alter enzyme activity, influencing the production of volatile compounds that determine flavor.
Correct answer is: Quantifying different splice variants of flavor‑related genes
Q.30 Which of the following is NOT a typical step in a bioinformatics workflow for detecting mycotoxins in grain using sequencing data?
Quality trimming of reads
Alignment to fungal reference genomes
Prediction of secondary metabolite gene clusters
Calculation of chlorophyll content
Explanation - Chlorophyll content is unrelated to sequencing‑based detection of mycotoxin‑producing fungi.
Correct answer is: Calculation of chlorophyll content
Q.31 In the analysis of plant‑microbe interactions, which bioinformatic approach helps identify secreted effector proteins from a pathogen genome?
Signal peptide prediction using tools like SignalP
Phylogenetic tree reconstruction
Gene expression heatmap generation
Metabolic pathway enrichment
Explanation - Effectors are usually secreted proteins; SignalP detects N‑terminal signal peptides indicative of secretion.
Correct answer is: Signal peptide prediction using tools like SignalP
Q.32 Which cloud‑based platform is widely used for sharing and reproducing bioinformatics analyses in agriculture?
Google Docs
Microsoft Azure Notebooks
CyVerse
Dropbox
Explanation - CyVerse offers computational resources, data storage, and workflow tools tailored for life‑science research, including agriculture.
Correct answer is: CyVerse
Q.33 What is the purpose of a ‘heat map’ in the context of gene expression studies for drought‑tolerant crops?
To display the geographic distribution of crops
To visualize the relative expression levels of many genes across samples
To calculate the total biomass
To predict rainfall patterns
Explanation - Heat maps provide an intuitive color‑coded representation of up‑ and down‑regulated genes across conditions.
Correct answer is: To visualize the relative expression levels of many genes across samples
Q.34 Which bioinformatic metric measures the completeness of a newly assembled plant genome?
N50
E‑value
GC content
BUSCO score
Explanation - BUSCO evaluates the presence of conserved single‑copy orthologs, indicating how complete the assembly is.
Correct answer is: BUSCO score
Q.35 A plant breeder wants to use a ‘genomic prediction model’ for yield. Which type of data is essential as input?
Soil texture measurements
High‑density SNP genotype matrix
Leaf shape images
Weather forecast data
Explanation - Genomic prediction models use SNP genotypes to estimate breeding values for quantitative traits like yield.
Correct answer is: High‑density SNP genotype matrix
Q.36 Which algorithm is commonly employed for clustering similar metagenomic reads into species‑level bins?
K‑means
MetaBAT
BWA
HMMER
Explanation - MetaBAT uses contig coverage and composition to bin metagenomic assemblies into putative genomes.
Correct answer is: MetaBAT
Q.37 What does the term ‘functional annotation’ refer to in the context of a newly sequenced plant genome?
Assigning chromosome numbers to scaffolds
Predicting the biological role of genes and proteins
Measuring the plant’s height
Calculating the genome’s GC content
Explanation - Functional annotation adds information about gene products, pathways, and cellular locations to raw sequence data.
Correct answer is: Predicting the biological role of genes and proteins
Q.38 Which type of bioinformatic analysis would help a food scientist determine if a new grain variety contains any novel toxic peptides?
Proteome-wide toxin prediction using tools like ToxinPred
Phylogenetic tree analysis
SNP density mapping
Metabolic flux balance analysis
Explanation - ToxinPred evaluates peptide sequences for characteristics associated with toxicity, useful for safety screening.
Correct answer is: Proteome-wide toxin prediction using tools like ToxinPred
Q.39 When using the software ‘PLINK’ in crop genetics, what is the primary purpose of the ––assoc flag?
To perform association testing between markers and traits
To assemble contigs
To predict protein structure
To visualize metabolic pathways
Explanation - The ––assoc command in PLINK runs basic case/control or quantitative trait association analyses.
Correct answer is: To perform association testing between markers and traits
Q.40 Which bioinformatics approach can be used to predict the effect of a single nucleotide change on the binding affinity of a transcription factor in a plant promoter?
Motif scanning with Position Weight Matrices (PWM)
RNA‑Seq differential expression
Protein 3‑D structure prediction
Metabolite profiling
Explanation - PWMs model TF binding preferences; scanning altered sequences reveals potential changes in affinity.
Correct answer is: Motif scanning with Position Weight Matrices (PWM)
Q.41 Which of the following is a major advantage of using a ‘cloud‑based Jupyter Notebook’ for bioinformatics training in agricultural universities?
It eliminates the need for any programming knowledge
It provides a ready‑to‑use environment with pre‑installed tools and collaborative features
It guarantees faster sequencing runs
It automatically writes research papers
Explanation - Jupyter Notebooks hosted on the cloud allow students to run code, visualize data, and share analyses without local installations.
Correct answer is: It provides a ready‑to‑use environment with pre‑installed tools and collaborative features
Q.42 In a study of the gut microbiome of silkworms fed on different mulberry leaves, which metric quantifies the diversity within a single sample?
Beta diversity
Alpha diversity
Gamma diversity
Delta diversity
Explanation - Alpha diversity measures species richness and evenness within a single community sample.
Correct answer is: Alpha diversity
Q.43 Which bioinformatics technique is most suitable for discovering novel enzymes involved in cellulose degradation in a newly sequenced fungal strain?
Homology modeling
Domain annotation using Pfam
SNP calling
Chromatin immunoprecipitation sequencing
Explanation - Pfam identifies protein families and domains such as glycoside hydrolases, pointing to enzymes that degrade cellulose.
Correct answer is: Domain annotation using Pfam
Q.44 Which statistical test is commonly applied to assess whether a set of differentially expressed genes is significantly enriched in a specific GO term?
Chi‑square test
Fisher’s exact test
Student’s t‑test
ANOVA
Explanation - Fisher’s exact test evaluates enrichment by comparing observed vs. expected counts of genes in a GO category.
Correct answer is: Fisher’s exact test
Q.45 A biotech company wants to develop a probiotic yogurt using a strain of Lactobacillus isolated from traditional cheese. Which bioinformatics step ensures the strain does not carry virulence genes?
Performing a BLAST search against the VFDB (Virulence Factor Database)
Constructing a phylogenetic tree
Estimating GC content
Running a de‑novo assembly
Explanation - Screening the genome against VFDB detects known virulence determinants, ensuring safety for consumption.
Correct answer is: Performing a BLAST search against the VFDB (Virulence Factor Database)
Q.46 Which of the following best describes a ‘k‑mer’ in the context of genome assembly?
A protein motif
A short DNA subsequence of length k
A type of sequencing error
A statistical model for expression
Explanation - K‑mers are substrings of length k used by assemblers to build overlap graphs and resolve repeats.
Correct answer is: A short DNA subsequence of length k
Q.47 In the analysis of a fruit’s nutritional profile, which bioinformatic resource helps map identified metabolites to known biosynthetic pathways?
KEGG Mapper
BLAST
MAFFT
FastQC
Explanation - KEGG Mapper visualizes metabolites within their corresponding enzymatic pathways, aiding interpretation of nutritional data.
Correct answer is: KEGG Mapper
Q.48 When performing a GWAS for disease resistance in barley, what does a ‘Manhattan plot’ display?
Geographic locations of fields
p‑values of marker‑trait associations across chromosomes
Temperature variations over time
Protein secondary structures
Explanation - A Manhattan plot shows the statistical significance of each SNP, with peaks indicating potential resistance loci.
Correct answer is: p‑values of marker‑trait associations across chromosomes
Q.49 Which tool would you use to predict the subcellular localization of a newly discovered plant protein involved in vitamin biosynthesis?
SignalP
TargetP
HMMER
Bowtie2
Explanation - TargetP predicts the likely destination of proteins (e.g., chloroplast, mitochondria) based on N‑terminal sequences.
Correct answer is: TargetP
Q.50 A farmer wants to monitor the spread of a fungal pathogen in real time using field‑deployed sensors. Which bioinformatics component is essential for this system?
On‑device read alignment and rapid taxonomic classification (e.g., using Kraken2)
3‑D protein modeling
Gene ontology enrichment
Metabolic flux simulation
Explanation - Kraken2 can classify sequencing reads in minutes, enabling immediate detection of pathogen DNA from sensor outputs.
Correct answer is: On‑device read alignment and rapid taxonomic classification (e.g., using Kraken2)
Q.51 Which of the following is a key limitation of using only 16S rRNA amplicon sequencing for food safety testing?
Inability to detect viruses
Low sequencing depth
High error rate in base calling
Difficulty in assembling plant genomes
Explanation - 16S rRNA targets bacterial ribosomal genes, so viral contaminants remain undetected.
Correct answer is: Inability to detect viruses
Q.52 What does the ‘E‑value’ indicate in a BLAST search against a pathogen database?
The expected number of random matches with similar score
The efficiency of the sequencing instrument
The expression level of the gene
The enzyme activity in the sample
Explanation - A lower E‑value suggests a more statistically significant alignment, reducing the chance of false positives.
Correct answer is: The expected number of random matches with similar score
Q.53 Which of the following bioinformatics methods can be employed to design primers that specifically amplify a gene variant conferring herbicide resistance?
In‑silico PCR using Primer‑BLAST
RNA‑Seq differential expression
Metagenomic binning
Protein docking simulation
Explanation - Primer‑BLAST allows users to design primers that uniquely match the target variant while avoiding off‑targets.
Correct answer is: In‑silico PCR using Primer‑BLAST
Q.54 In the context of agricultural bioinformatics, what is a ‘digital twin’?
A cloned plant grown in a lab
A computational replica of a farm or crop system that integrates multi‑omics and sensor data
A type of genetic marker
A software for designing irrigation channels
Explanation - Digital twins simulate real‑world agricultural processes, enabling scenario testing and optimization.
Correct answer is: A computational replica of a farm or crop system that integrates multi‑omics and sensor data
Q.55 Which data visualization technique is most appropriate for showing the relationship between gene expression levels of stress‑responsive genes and different temperature treatments?
Box plot
Scatter plot with regression line
Venn diagram
Stacked bar chart
Explanation - Scatter plots illustrate continuous relationships between expression (y‑axis) and temperature (x‑axis), and regression lines highlight trends.
Correct answer is: Scatter plot with regression line
Q.56 A scientist wants to identify gene clusters responsible for the synthesis of a novel antioxidant in berries. Which bioinformatics pipeline would be most effective?
AntiSMASH for secondary metabolite gene cluster detection
Bowtie2 alignment to a reference genome
FastQC quality control
GATK variant filtration
Explanation - AntiSMASH predicts biosynthetic gene clusters, aiding discovery of pathways for specialized metabolites.
Correct answer is: AntiSMASH for secondary metabolite gene cluster detection
Q.57 Which of the following is a major benefit of integrating transcriptomic and metabolomic data when evaluating the nutritional quality of a new grain variety?
It reduces the need for field trials
It provides a holistic view linking gene activity to metabolite accumulation
It eliminates the need for sequencing
It automatically predicts consumer acceptance
Explanation - Combined omics reveal how transcriptional changes drive metabolic outputs that determine nutritional traits.
Correct answer is: It provides a holistic view linking gene activity to metabolite accumulation
Q.58 Which of the following best describes the purpose of ‘linkage mapping’ in plant breeding?
To locate QTLs by analyzing recombination frequencies between markers
To measure photosynthetic efficiency
To calculate soil nutrient content
To predict climate change impacts
Explanation - Linkage maps order markers based on recombination, allowing identification of quantitative trait loci (QTLs).
Correct answer is: To locate QTLs by analyzing recombination frequencies between markers
Q.59 When analyzing a large set of SNPs for population structure in a crop, which software is commonly used to perform principal component analysis (PCA)?
PLINK
MEGA
Clustal Omega
PHYLIP
Explanation - PLINK includes functions for PCA, which visualizes genetic relationships among individuals.
Correct answer is: PLINK
Q.60 Which bioinformatic approach can be used to predict whether a newly discovered peptide from a fermented food is a potential antimicrobial agent?
Using the CAMP (Collection of Anti‑Microbial Peptides) prediction tool
Running a de‑novo genome assembly
Performing a GWAS
Constructing a phylogenetic tree
Explanation - CAMP predicts antimicrobial activity based on sequence features of known peptides.
Correct answer is: Using the CAMP (Collection of Anti‑Microbial Peptides) prediction tool
Q.61 Which of the following describes a ‘gene drive’ that could be applied to control pest insects affecting crops?
A technique that increases the frequency of a desired allele through biased inheritance
A method for measuring soil moisture
A way to annotate plant genomes
A statistical test for association
Explanation - Gene drives bias inheritance so a particular trait spreads rapidly through a population, useful for pest control.
Correct answer is: A technique that increases the frequency of a desired allele through biased inheritance
Q.62 In a study of the effect of post‑harvest storage on fruit quality, which omics technology would most directly assess changes in volatile aroma compounds?
Metabolomics using GC‑MS
RNA‑Seq
ChIP‑Seq
SNP genotyping
Explanation - Gas chromatography‑mass spectrometry profiles volatile metabolites that contribute to aroma.
Correct answer is: Metabolomics using GC‑MS
Q.63 Which of the following is a common format for representing variant call data after sequencing?
VCF
BED
GTF
FASTA
Explanation - Variant Call Format (VCF) stores SNPs, indels, and structural variants along with metadata.
Correct answer is: VCF
Q.64 A researcher wants to visualize the distribution of a specific SNP across different rice cultivars worldwide. Which tool would be most suitable?
ArcGIS
iTOL (Interactive Tree Of Life)
Genome Browser with custom track
RStudio
Explanation - Custom tracks in genome browsers can display SNP frequencies across geographic samples.
Correct answer is: Genome Browser with custom track
Q.65 Which of the following is NOT typically a step in a standard RNA‑Seq workflow for plants?
Read alignment to a reference transcriptome
Differential expression analysis
Protein crystallization
Quality control with FastQC
Explanation - Protein crystallization is unrelated to RNA‑Seq, which focuses on RNA molecules.
Correct answer is: Protein crystallization
Q.66 When using a hidden Markov model (HMM) to identify disease‑resistance gene families in a crop genome, which database provides curated HMM profiles?
Pfam
NCBI SRA
EMBL‑EBI MetaboLights
PDB
Explanation - Pfam contains HMM profiles for protein families, useful for scanning genomes for specific domains.
Correct answer is: Pfam
Q.67 Which method is commonly used to validate bioinformatic predictions of gene function in the laboratory?
qPCR to confirm expression patterns
Electron microscopy
Chromatography
Spectrophotometry
Explanation - Quantitative PCR measures transcript levels, validating computational predictions about gene activity.
Correct answer is: qPCR to confirm expression patterns
Q.68 In a bioinformatics pipeline for detecting food‑borne pathogens, what is the purpose of the ‘host‑removal’ step?
To delete irrelevant data files
To filter out reads that map to the host (e.g., human or plant) genome, focusing on microbial reads
To increase sequencing depth
To generate phylogenetic trees
Explanation - Removing host DNA reduces background noise, improving detection of low‑abundance pathogens.
Correct answer is: To filter out reads that map to the host (e.g., human or plant) genome, focusing on microbial reads
Q.69 Which metric is used to assess the similarity between two protein sequences after alignment?
E‑value
Identity percentage
Read length
Coverage depth
Explanation - Identity percentage reflects the proportion of exactly matching residues in the alignment.
Correct answer is: Identity percentage
Q.70 A plant pathologist wants to predict the emergence of a new rust strain. Which bioinformatics technique combines sequence data with epidemiological modeling?
Phylodynamics
Gene set enrichment analysis
Metabolic flux analysis
Protein docking
Explanation - Phylodynamics integrates phylogenetics with population dynamics to forecast pathogen spread.
Correct answer is: Phylodynamics
Q.71 Which of the following is a primary advantage of using a ‘graph genome’ over a linear reference for crop breeding applications?
Simpler data storage
Better representation of genetic variation across multiple varieties
Faster sequencing run times
Elimination of the need for annotation
Explanation - Graph genomes embed multiple haplotypes, reducing reference bias and improving variant discovery.
Correct answer is: Better representation of genetic variation across multiple varieties
Q.72 In the context of food biotechnology, what is the role of the ‘FAIR’ principles?
Ensuring data is Findable, Accessible, Interoperable, and Reusable
Measuring the freshness of produce
Standardizing irrigation schedules
Classifying soil types
Explanation - FAIR principles guide responsible data management, facilitating sharing and reproducibility in bioinformatics.
Correct answer is: Ensuring data is Findable, Accessible, Interoperable, and Reusable
Q.73 Which type of sequencing is most appropriate for profiling the active microbial community (i.e., metabolically active cells) in a fermented beverage?
16S rRNA amplicon sequencing of DNA
Metatranscriptomics (RNA‑Seq of community RNA)
Whole‑genome shotgun sequencing of host DNA
ChIP‑Seq
Explanation - Metatranscriptomics captures expressed genes, indicating which microbes are actively metabolizing.
Correct answer is: Metatranscriptomics (RNA‑Seq of community RNA)
Q.74 Which of the following tools is specifically designed for visualizing large phylogenetic trees with associated metadata?
iTOL
FastQC
BWA
Trimmomatic
Explanation - Interactive Tree Of Life (iTOL) allows annotation of trees with colors, shapes, and external data.
Correct answer is: iTOL
Q.75 A bioinformatic analysis identified a set of genes up‑regulated under nitrogen deficiency in maize. Which downstream experiment would best confirm their functional role?
Create knock‑out mutants using CRISPR and assess growth under low nitrogen
Measure soil nitrogen levels
Perform a Western blot for unrelated proteins
Sequence the chloroplast genome
Explanation - Targeted gene knock‑outs test causality by observing phenotypic effects under the same stress condition.
Correct answer is: Create knock‑out mutants using CRISPR and assess growth under low nitrogen
Q.76 Which bioinformatic method is commonly employed to identify potential off‑target sites when designing CRISPR guides for a crop genome?
BLAST against the whole genome
FastQC quality check
RNA‑Seq expression profiling
Phylogenetic tree construction
Explanation - Aligning the guide RNA sequence to the genome reveals similar sites that could be unintentionally edited.
Correct answer is: BLAST against the whole genome
Q.77 Which of the following best explains why ‘gene expression normalization’ (e.g., TPM, RPKM) is necessary in RNA‑Seq analysis?
To adjust for differences in sequencing depth and gene length
To change the DNA sequence
To increase the number of reads
To convert RNA to protein
Explanation - Normalization makes expression values comparable across samples and genes.
Correct answer is: To adjust for differences in sequencing depth and gene length
Q.78 A researcher wants to assess the impact of a new fertilizer on the metabolic pathways of wheat kernels. Which pathway analysis tool would be most appropriate?
KEGG Mapper
BLAST
MAFFT
GATK
Explanation - KEGG Mapper visualizes changes in metabolic pathways based on gene or metabolite data.
Correct answer is: KEGG Mapper
Q.79 Which of the following is a typical output of a ‘variant effect predictor’ (VEP) when applied to crop SNP data?
Predicted impact of each SNP on gene function (e.g., missense, synonymous)
Phylogenetic tree of the species
Heat map of soil moisture
3‑D protein structures
Explanation - VEP annotates variants with functional consequences, helping prioritize candidates for breeding.
Correct answer is: Predicted impact of each SNP on gene function (e.g., missense, synonymous)
Q.80 In the context of bioinformatics pipelines, what does the term ‘workflow orchestration’ refer to?
The arrangement of computational steps and their dependencies to run automatically
The manual execution of each command line tool
The physical layout of a laboratory bench
The design of agricultural equipment
Explanation - Workflow orchestration tools (e.g., Nextflow, Snakemake) manage complex pipelines, ensuring reproducibility.
Correct answer is: The arrangement of computational steps and their dependencies to run automatically
Q.81 Which of the following best describes the purpose of ‘eQTL mapping’ in crop genomics?
Linking expression levels of genes to specific genetic loci
Measuring electrical conductivity of soil
Determining the color of fruit skins
Estimating harvest dates
Explanation - Expression quantitative trait loci (eQTL) associate genetic variation with gene expression differences.
Correct answer is: Linking expression levels of genes to specific genetic loci
Q.82 A food scientist wants to predict the shelf‑life of a packaged snack based on microbial succession data. Which type of model is most appropriate?
Time‑series forecasting (e.g., ARIMA) on microbial abundance data
Phylogenetic tree reconstruction
Protein secondary structure prediction
Genome assembly
Explanation - Time‑series models can extrapolate microbial growth trends to estimate spoilage timelines.
Correct answer is: Time‑series forecasting (e.g., ARIMA) on microbial abundance data
Q.83 Which of the following is a key challenge when applying bioinformatics to polyploid crops like wheat?
Distinguishing homoeologous gene copies during assembly and variant calling
Lack of any DNA sequencing technologies
Inability to grow wheat in a lab
Absence of any metabolic pathways
Explanation - Polyploid genomes contain multiple similar copies of genes, complicating accurate assembly and SNP detection.
Correct answer is: Distinguishing homoeologous gene copies during assembly and variant calling
Q.84 Which of the following best describes ‘metabolic flux analysis’ in the context of engineered food microbes?
Quantitative estimation of the rates of biochemical reactions in a metabolic network
Measuring the electrical conductivity of a broth
Counting the number of cells under a microscope
Sequencing the genome of the microbe
Explanation - Flux analysis helps optimize production pathways for desired metabolites in engineered microbes.
Correct answer is: Quantitative estimation of the rates of biochemical reactions in a metabolic network
Q.85 A researcher is comparing two tomato varieties for resistance to a bacterial blight. Which statistical method is most suitable for testing whether the observed difference in disease scores is significant?
Student’s t‑test
Principal Component Analysis
Hidden Markov Model
BLAST
Explanation - The t‑test compares the means of two groups to assess if the difference is unlikely due to random variation.
Correct answer is: Student’s t‑test
Q.86 Which of the following databases specializes in plant-specific metabolic pathways and enzymes?
PlantCyc
Pfam
RCSB PDB
NCBI SRA
Explanation - PlantCyc curates curated metabolic pathways specific to plants, supporting functional genomics studies.
Correct answer is: PlantCyc
Q.87 When using the ‘edgeR’ package for differential expression analysis, what does the term ‘dispersion’ refer to?
The variability of gene expression counts beyond Poisson noise
The physical distance between two genes on a chromosome
The length of DNA fragments
The temperature of the incubator
Explanation - Dispersion estimates how much observed counts deviate from the expected Poisson distribution, influencing statistical power.
Correct answer is: The variability of gene expression counts beyond Poisson noise
Q.88 Which of the following best explains why ‘cross‑validation’ is important when building a machine‑learning model to predict crop yield from genomic data?
It tests model performance on unseen data, reducing over‑fitting
It increases the number of SNPs
It changes the DNA sequence of the plant
It reduces the cost of sequencing
Explanation - Cross‑validation partitions data into training and testing sets, providing an unbiased estimate of predictive accuracy.
Correct answer is: It tests model performance on unseen data, reducing over‑fitting
Q.89 A bioinformatician wants to compare the microbial composition of raw milk versus pasteurized milk. Which metric would best capture differences in community structure?
Bray‑Curtis dissimilarity
GC content
Read length distribution
Nucleotide substitution rate
Explanation - Bray‑Curtis quantifies compositional differences between two ecological samples based on abundance data.
Correct answer is: Bray‑Curtis dissimilarity
Q.90 Which of the following is a primary benefit of integrating IoT sensor data with genomic information in precision agriculture?
Enabling real‑time, genotype‑guided management decisions (e.g., variable fertilizer application)
Automatically editing the plant genome
Predicting global market trends
Replacing the need for field experiments
Explanation - Combining genotype data with environmental sensors allows tailored agronomic practices that match plant genetic potential.
Correct answer is: Enabling real‑time, genotype‑guided management decisions (e.g., variable fertilizer application)
Q.91 Which of the following tools is designed specifically for rapid taxonomic classification of short reads in metagenomic food safety applications?
Kraken2
BWA-MEM
MAFFT
GATK
Explanation - Kraken2 uses exact k‑mer matches to assign reads to taxa in milliseconds, ideal for quick pathogen detection.
Correct answer is: Kraken2
Q.92 What is the main purpose of a ‘heat‑stable enzyme’ annotation in a database of fruit‑derived proteins?
To indicate that the enzyme retains activity after pasteurization, making it useful for food processing
To show that the enzyme is only active at low temperatures
To prove that the fruit is genetically modified
To measure the fruit's sugar content
Explanation - Heat‑stable enzymes can survive processing steps, offering functional benefits in industrial food applications.
Correct answer is: To indicate that the enzyme retains activity after pasteurization, making it useful for food processing
Q.93 Which of the following is an example of a ‘synthetic biology’ application in agriculture that relies on bioinformatics?
Designing a synthetic metabolic pathway in microbes to produce vitamin‑rich plant extracts
Measuring soil pH with a handheld meter
Using drones to monitor crop height
Applying traditional cross‑pollination techniques
Explanation - Synthetic biology uses computational design of gene circuits to engineer microbes that biosynthesize valuable compounds for food.
Correct answer is: Designing a synthetic metabolic pathway in microbes to produce vitamin‑rich plant extracts
Q.94 When visualizing SNP density across a chromosome, which plot type is most appropriate?
Manhattan plot
Heat map
Box plot
Pie chart
Explanation - Manhattan plots display the distribution and significance of SNPs along chromosomes, often used in GWAS and density visualizations.
Correct answer is: Manhattan plot
Q.95 Which bioinformatic approach would you use to infer the evolutionary origin of a newly discovered gene that appears only in a domesticated legume?
Phylogenetic reconstruction with outgroup species
RNA‑Seq differential expression analysis
Metabolite profiling
SNP calling
Explanation - Including outgroup taxa helps determine whether the gene is a recent acquisition, duplication, or horizontal transfer.
Correct answer is: Phylogenetic reconstruction with outgroup species
Q.96 Which of the following statements about the ‘FASTA’ file format is true?
It stores sequence identifiers preceded by a ‘>’ character followed by the sequence on the next line(s)
It contains quality scores for each base
It is only used for protein structures
It is a binary format
Explanation - FASTA files begin with a header line starting with ‘>’, followed by one or more lines of the nucleotide or protein sequence.
Correct answer is: It stores sequence identifiers preceded by a ‘>’ character followed by the sequence on the next line(s)
Q.97 A researcher wants to predict the impact of a SNP on a protein’s stability. Which computational tool is commonly used for this purpose?
FoldX
Bowtie2
Trimmomatic
FastQC
Explanation - FoldX estimates changes in protein free energy caused by amino‑acid substitutions, indicating stability effects.
Correct answer is: FoldX
Q.98 Which of the following is a limitation of using short‑read Illumina data for assembling highly repetitive plant genomes?
Inability to span long repeat regions, leading to fragmented assemblies
Excessively high error rates
Requirement for large DNA quantities
Incompatibility with any bioinformatics software
Explanation - Short reads cannot bridge repeats longer than the read length, causing gaps and misassemblies.
Correct answer is: Inability to span long repeat regions, leading to fragmented assemblies
Q.99 What does the term ‘phenomics’ refer to in modern crop research?
High‑throughput measurement of plant traits using sensors and imaging
Sequencing of plant genomes
Cultivation of plants in hydroponic systems
Application of fertilizer
Explanation - Phenomics captures large‑scale phenotypic data, often linked to genomic information for breeding.
Correct answer is: High‑throughput measurement of plant traits using sensors and imaging
Q.100 Which of the following is a typical output of the ‘KEGG enrichment’ analysis performed on a list of differentially expressed genes?
A ranked list of metabolic pathways that are over‑represented
A phylogenetic tree of the species
A heat map of soil moisture
A 3‑D model of the plant
Explanation - KEGG enrichment identifies pathways with more member genes than expected by chance, highlighting biological processes involved.
Correct answer is: A ranked list of metabolic pathways that are over‑represented
Q.101 A biotech company is developing a probiotic cheese starter culture. Which bioinformatic analysis would be crucial to ensure the strain does not carry antibiotic‑resistance genes?
Screening the genome against the ResFinder database
Performing a de‑novo assembly of the cheese genome
Running a GWAS on milk yield
Conducting a phylogenetic analysis of dairy cows
Explanation - ResFinder identifies known resistance genes, ensuring the probiotic strain meets safety standards.
Correct answer is: Screening the genome against the ResFinder database
Q.102 Which of the following best describes a ‘haplotype block’ in crop genetics?
A region of the genome where recombination is low and a set of alleles are inherited together
A group of plants grown together in a field
A collection of soil samples
A type of fertilizer
Explanation - Haplotype blocks simplify genetic analyses by treating linked SNPs as a single unit.
Correct answer is: A region of the genome where recombination is low and a set of alleles are inherited together
Q.103 Which of the following is an example of a ‘synthetic promoter’ designed using bioinformatics for enhanced expression of a vitamin‑C biosynthesis gene in tomato?
A promoter sequence engineered by combining strong cis‑regulatory elements identified from multiple species
A promoter that naturally occurs in wild tomatoes
A random DNA sequence
A promoter derived from bacterial ribosomal RNA
Explanation - Synthetic promoters are constructed in silico by assembling known regulatory motifs to achieve desired expression levels.
Correct answer is: A promoter sequence engineered by combining strong cis‑regulatory elements identified from multiple species
Q.104 When analyzing the microbial community of a fermented soy product, which diversity metric would you use to compare community composition between two different fermentation batches?
Beta diversity (e.g., Bray‑Curtis distance)
Alpha diversity
GC content
Read length distribution
Explanation - Beta diversity quantifies differences in species composition between samples, useful for batch comparison.
Correct answer is: Beta diversity (e.g., Bray‑Curtis distance)
Q.105 Which of the following statements about the ‘FAIR’ principles is FALSE?
FAIR encourages data to be Findable, Accessible, Interoperable, and Reusable
FAIR mandates that all data must be stored on local hard drives
FAIR promotes use of standardized metadata
FAIR improves reproducibility of scientific analyses
Explanation - FAIR does not prescribe storage location; it focuses on data accessibility and interoperability, often via cloud repositories.
Correct answer is: FAIR mandates that all data must be stored on local hard drives
Q.106 A researcher wants to predict how a new allele will affect plant height in maize using existing genotype‑phenotype data. Which type of model is most appropriate?
Genomic best linear unbiased prediction (GBLUP)
Linear discriminant analysis for classification
K‑means clustering
Hidden Markov Model for sequence alignment
Explanation - GBLUP leverages genome‑wide marker effects to predict quantitative traits like plant height.
Correct answer is: Genomic best linear unbiased prediction (GBLUP)
Q.107 Which of the following tools can be used to predict the subcellular localization of a plant protein that may be secreted into the apoplast?
TargetP
BWA
FastQC
Trimmomatic
Explanation - TargetP predicts signal peptides and destination compartments such as secretory pathways.
Correct answer is: TargetP
Q.108 When performing a genome‑wide association study (GWAS) for fruit sweetness, what does a ‘significant peak’ on a Manhattan plot indicate?
A genomic region where SNPs are strongly associated with the trait
The exact sweetness level of the fruit
The temperature at which the fruit was harvested
The number of chromosomes in the species
Explanation - Significant peaks reflect loci that potentially harbor genes influencing the phenotype of interest.
Correct answer is: A genomic region where SNPs are strongly associated with the trait
Q.109 Which of the following best describes the concept of ‘precision fermentation’ in food biotechnology?
Engineering microorganisms to produce specific food ingredients (e.g., proteins, flavors) at scale using bioinformatics‑guided design
Fermenting food without any microbes
Using only traditional starter cultures without genetic modification
Measuring fermentation temperature manually
Explanation - Precision fermentation combines synthetic biology and computational design to manufacture targeted food components.
Correct answer is: Engineering microorganisms to produce specific food ingredients (e.g., proteins, flavors) at scale using bioinformatics‑guided design
Q.110 Which of the following is an example of a ‘multi‑omics’ integration strategy in crop improvement?
Combining transcriptomics, metabolomics, and phenomics data to identify candidate genes for stress tolerance
Using only soil nutrient data
Sequencing only the chloroplast genome
Measuring leaf length with a ruler
Explanation - Multi‑omics integrates diverse data layers to provide a comprehensive view of genotype‑phenotype relationships.
Correct answer is: Combining transcriptomics, metabolomics, and phenomics data to identify candidate genes for stress tolerance
Q.111 What is the primary purpose of a ‘reference genome’ in agricultural bioinformatics?
To provide a scaffold for aligning sequencing reads and identifying variants
To serve as a physical seed bank
To replace the need for field trials
To measure soil pH
Explanation - A reference genome acts as a coordinate system for mapping reads, calling variants, and annotating functional elements.
Correct answer is: To provide a scaffold for aligning sequencing reads and identifying variants
Q.112 A plant breeder is interested in a gene that confers resistance to a fungal pathogen. Which bioinformatic approach can help identify candidate resistance (R) genes in the genome?
Search for NBS‑LRR domain-containing genes using HMM profiles from Pfam
Calculate the GC content of the whole genome
Measure leaf chlorophyll content
Perform a soil texture analysis
Explanation - R genes often contain nucleotide‑binding site (NBS) and leucine‑rich repeat (LRR) domains; HMM searches can locate them.
Correct answer is: Search for NBS‑LRR domain-containing genes using HMM profiles from Pfam
Q.113 Which of the following best describes the purpose of ‘k‑mer counting’ in genome assembly quality assessment?
To evaluate coverage uniformity and detect sequencing errors or contamination
To predict protein tertiary structure
To measure leaf area index
To calculate irrigation requirements
Explanation - K‑mer frequency spectra reveal issues like uneven coverage, repeats, or foreign DNA in sequencing data.
Correct answer is: To evaluate coverage uniformity and detect sequencing errors or contamination
Q.114 In a study of drought‑responsive genes, a researcher identifies a transcription factor binding motif that is enriched in promoter regions. Which tool can be used to discover such motifs?
MEME Suite
BWA-MEM
FastQC
SAMtools
Explanation - MEME discovers statistically over‑represented motifs in a set of sequences, useful for regulatory element analysis.
Correct answer is: MEME Suite
Q.115 Which of the following is a common challenge when using metagenomic data to assess food safety?
Distinguishing closely related pathogenic strains amid a complex background of harmless microbes
Lack of any DNA in food samples
Inability to sequence bacterial DNA
Excessively low sequencing costs
Explanation - High similarity among strains makes accurate identification of pathogens difficult, requiring sensitive classification methods.
Correct answer is: Distinguishing closely related pathogenic strains amid a complex background of harmless microbes
Q.116 Which of the following statements about ‘gene drives’ is FALSE?
Gene drives can spread a genetic trait through a population faster than Mendelian inheritance
Gene drives guarantee 100% success in every species
Gene drives raise ecological and ethical concerns
Gene drives can be used for pest population control
Explanation - Gene drives are not universally effective; success depends on biology, resistance evolution, and ecological factors.
Correct answer is: Gene drives guarantee 100% success in every species
Q.117 In the analysis of a new apple cultivar’s genome, a scientist observes a high proportion of duplicated genes. Which evolutionary process most likely explains this observation?
Whole‑genome duplication (polyploidy)
Horizontal gene transfer from bacteria
RNA interference
Methylation of DNA
Explanation - Polyploid events duplicate the entire set of chromosomes, leading to many duplicated genes in the genome.
Correct answer is: Whole‑genome duplication (polyploidy)
Q.118 Which bioinformatic resource would you use to predict potential off‑target cleavage sites for a CRISPR guide RNA designed for soybean?
CRISPOR
FastQC
MEGA
Trimmomatic
Explanation - CRISPOR evaluates guide RNA specificity and lists genomic locations with similarity that could be off‑targets.
Correct answer is: CRISPOR
Q.119 A scientist wants to compare the expression of a set of genes across multiple fruit developmental stages. Which visualization best summarizes this data?
Heat map
Manhattan plot
Phylogenetic tree
Venn diagram
Explanation - Heat maps display expression levels (e.g., color intensity) across samples, making patterns easy to see.
Correct answer is: Heat map
Q.120 Which of the following is a typical output of the ‘GATK HaplotypeCaller’ when analyzing plant sequencing data?
A VCF file containing variant calls and genotype information
A phylogenetic tree of plant species
A 3‑D model of a protein
A list of soil nutrients
Explanation - HaplotypeCaller identifies SNPs and indels and records them in the Variant Call Format (VCF).
Correct answer is: A VCF file containing variant calls and genotype information
Q.121 Which of the following best describes a ‘digital phenotype’ in precision agriculture?
Quantitative trait data captured by sensors (e.g., canopy temperature, NDVI) and stored digitally
A handwritten note of plant height
The DNA sequence of a plant
The taste of a fruit
Explanation - Digital phenotypes are sensor‑derived measurements that can be linked with genomic data for analysis.
Correct answer is: Quantitative trait data captured by sensors (e.g., canopy temperature, NDVI) and stored digitally
Q.122 Which of the following tools can be used to predict the antimicrobial activity of a peptide discovered in a fermented dairy product?
APD3 (Antimicrobial Peptide Database) prediction tool
BWA
MAFFT
GATK
Explanation - APD3 provides algorithms to assess peptide sequences for antimicrobial properties.
Correct answer is: APD3 (Antimicrobial Peptide Database) prediction tool
Q.123 What is the main advantage of using a ‘graph database’ (e.g., Neo4j) to store plant genotype‑phenotype relationships?
Efficiently model complex many‑to‑many relationships and enable fast traversals for queries
It reduces the size of the genome sequence
It automatically predicts weather patterns
It eliminates the need for any statistical analysis
Explanation - Graph databases excel at representing interconnected data, such as genes linked to multiple traits and environments.
Correct answer is: Efficiently model complex many‑to‑many relationships and enable fast traversals for queries
Q.124 Which of the following best explains why ‘batch effect correction’ is important in RNA‑Seq experiments comparing different crop varieties?
It removes technical variability unrelated to biological differences, improving the accuracy of differential expression results
It increases the number of reads generated
It changes the DNA sequence of the plants
It measures soil moisture
Explanation - Batch effects can confound true biological signals; correction methods (e.g., ComBat) adjust for these artifacts.
Correct answer is: It removes technical variability unrelated to biological differences, improving the accuracy of differential expression results
Q.125 A bioinformatician is tasked with identifying gene families involved in lignin biosynthesis across multiple grass species. Which tool would be most suitable?
OrthoFinder
FastQC
BWA
Trimmomatic
Explanation - OrthoFinder groups orthologous genes across species, facilitating identification of conserved biosynthetic families.
Correct answer is: OrthoFinder
Q.126 Which of the following statements about ‘synthetic promoters’ is TRUE?
They can be designed in silico by combining known regulatory motifs to achieve desired expression strength
They are always derived from bacterial DNA
They cannot be used in plants
They are unrelated to gene expression
Explanation - Synthetic promoters are engineered sequences that control transcription levels, often built from characterized motifs.
Correct answer is: They can be designed in silico by combining known regulatory motifs to achieve desired expression strength
Q.127 When performing a de‑novo assembly of a fungal genome used in cheese ripening, which metric indicates the continuity of the assembly?
N50
E‑value
GC content
Read depth
Explanation - N50 is the length at which 50% of the assembly is contained in contigs of that length or longer; higher N50 means more continuous assembly.
Correct answer is: N50
Q.128 Which of the following best describes the role of ‘metabolic modeling’ in bioengineered food microbes?
Predicting the flow of metabolites through pathways to optimize production yields
Measuring the pH of the growth medium
Counting the number of cells under a microscope
Sequencing the host plant genome
Explanation - Constraint‑based metabolic models (e.g., FBA) simulate how changes in enzyme levels affect product formation.
Correct answer is: Predicting the flow of metabolites through pathways to optimize production yields
Q.129 In a genome annotation pipeline, which step assigns functional descriptions to predicted protein‑coding genes?
Functional annotation using InterProScan
Read trimming with Trimmomatic
Quality control with FastQC
Assembly with SPAdes
Explanation - InterProScan integrates multiple protein signature databases to provide GO terms, domains, and functional predictions.
Correct answer is: Functional annotation using InterProScan
Q.130 Which of the following best illustrates the concept of ‘data provenance’ in bioinformatics workflows for food safety?
Tracking the origin, processing steps, and versions of all data files from raw reads to final reports
Measuring the temperature of a refrigerator
Counting the number of fruits on a tree
Recording the color of the laboratory walls
Explanation - Provenance ensures transparency, reproducibility, and trust in analytical results, critical for regulatory compliance.
Correct answer is: Tracking the origin, processing steps, and versions of all data files from raw reads to final reports
Q.131 A researcher wants to identify novel small RNAs involved in seed dormancy. Which sequencing approach is most appropriate?
Small‑RNA‑seq (sRNA‑seq)
Whole‑genome shotgun sequencing
ChIP‑seq
RNA‑seq of poly‑A mRNA
Explanation - sRNA‑seq captures short non‑coding RNAs (e.g., miRNAs) that regulate gene expression during dormancy.
Correct answer is: Small‑RNA‑seq (sRNA‑seq)
Q.132 Which of the following is a key consideration when designing a field trial to validate bioinformatic predictions of a drought‑tolerance gene?
Including multiple environmental replicates and appropriate controls to account for variability
Using only one plant per plot
Measuring only leaf color
Avoiding any statistical analysis
Explanation - Replication and controls ensure that observed effects are due to the gene and not random environmental factors.
Correct answer is: Including multiple environmental replicates and appropriate controls to account for variability
Q.133 Which bioinformatics method can be used to predict potential off‑target effects of a CRISPR edit on the microbiome present in fermented foods?
In‑silico off‑target analysis against microbial genome databases
Metabolite profiling
Leaf chlorophyll measurement
Soil moisture sensing
Explanation - Screening guide RNAs against known microbial genomes helps avoid unintended edits that could affect fermentation.
Correct answer is: In‑silico off‑target analysis against microbial genome databases
Q.134 A scientist discovers a novel gene cluster in a berry that may synthesize an antioxidant. Which bioinformatics resource can help predict the chemical structure of the resulting compound?
AntiSMASH coupled with NPAtlas
FastQC
BWA-MEM
Trimmomatic
Explanation - AntiSMASH predicts secondary metabolite gene clusters, and NPAtlas provides reference structures for comparison.
Correct answer is: AntiSMASH coupled with NPAtlas
Q.135 Which of the following statements about ‘gene set enrichment analysis’ (GSEA) is FALSE?
GSEA requires a predefined list of differentially expressed genes
GSEA evaluates whether predefined gene sets show statistically significant, coordinated differences between two biological states
GSEA can identify pathways that are modestly but consistently regulated
GSEA does not rely on arbitrary significance thresholds
Explanation - GSEA works on ranked whole‑genome expression data, avoiding strict cut‑offs for DE genes.
Correct answer is: GSEA requires a predefined list of differentially expressed genes
Q.136 Which of the following best describes the purpose of ‘phylogenetic profiling’ in the context of discovering novel plant enzymes?
Identifying genes that co‑occur across multiple genomes, suggesting a shared functional pathway
Measuring soil nitrogen levels
Counting the number of fruits per plant
Assessing leaf temperature
Explanation - Phylogenetic profiling infers functional associations by examining presence/absence patterns across species.
Correct answer is: Identifying genes that co‑occur across multiple genomes, suggesting a shared functional pathway
Q.137 A researcher wants to predict how a specific SNP will affect splicing of a gene involved in flavor production. Which tool would be appropriate?
SpliceAI
BWA
MAFFT
FastQC
Explanation - SpliceAI uses deep learning to predict changes in splice site strength caused by sequence variants.
Correct answer is: SpliceAI
Q.138 Which of the following is a primary reason to store agricultural genomic data in a public repository like NCBI's SRA?
To promote data sharing, reproducibility, and enable secondary analyses by the scientific community
To increase the cost of research
To hide the data from competitors
To limit access to only the original research team
Explanation - Public repositories ensure transparency, foster collaboration, and allow validation of results.
Correct answer is: To promote data sharing, reproducibility, and enable secondary analyses by the scientific community
Q.139 Which of the following best explains why ‘machine‑learning feature selection’ is important when building a model to predict crop yield from thousands of SNPs?
It reduces dimensionality, focusing on the most informative markers and improving model performance
It increases the number of SNPs used
It changes the DNA sequence of the plant
It measures soil temperature
Explanation - Feature selection removes redundant or noisy variables, preventing over‑fitting and speeding up training.
Correct answer is: It reduces dimensionality, focusing on the most informative markers and improving model performance
Q.140 A bioinformatician is tasked with integrating weather data, soil sensor readings, and genotype information to predict wheat rust outbreaks. Which type of model is most appropriate?
A multi‑modal machine‑learning model (e.g., random forest or gradient boosting) that can handle heterogeneous data types
A simple linear regression on soil pH alone
A protein structure prediction algorithm
A phylogenetic tree of wheat varieties
Explanation - Multi‑modal models can combine diverse inputs (genomic, environmental) to make robust disease predictions.
Correct answer is: A multi‑modal machine‑learning model (e.g., random forest or gradient boosting) that can handle heterogeneous data types
Q.141 Which of the following is a common output of a ‘pathway enrichment analysis’ performed on metabolites identified in a new fruit variety?
A list of metabolic pathways that are significantly over‑represented among the detected metabolites
A phylogenetic tree of the fruit species
A heat map of soil nutrients
A 3‑D rendering of the fruit
Explanation - Pathway enrichment highlights which biochemical routes are most active or altered in the sample.
Correct answer is: A list of metabolic pathways that are significantly over‑represented among the detected metabolites
Q.142 In the context of food safety, what does the term ‘bioinformatics‑driven hazard identification’ refer to?
Using computational analysis of genomic and metagenomic data to detect known or novel pathogens and toxins in food products
Measuring the temperature of a refrigerator
Counting the number of packages on a shelf
Assessing the taste of a food item
Explanation - Bioinformatics enables rapid identification of hazardous microorganisms or genes from sequencing data, improving safety monitoring.
Correct answer is: Using computational analysis of genomic and metagenomic data to detect known or novel pathogens and toxins in food products