Introduction to Bioinformatics MCQs With Answer

Introduction to Bioinformatics MCQs With Answer

Bioinformatics integrates biology, computer science, and statistics to analyze biological data relevant to pharmacy and drug development. This introduction covers key concepts such as sequence alignment, genomic and proteomic databases (GenBank, UniProt), BLAST searches, molecular docking, cheminformatics, NGS data, structural bioinformatics (PDB), homology modeling, and pathway analysis. B. Pharm students will learn how bioinformatics aids target identification, ADMET prediction, QSAR, and pharmacogenomics. These MCQs emphasize practical tools, data formats (FASTA, FASTQ, SAM/BAM), and algorithms (Needleman–Wunsch, Smith–Waterman) essential for pharmaceutical research and coursework. Now let’s test your knowledge with 30 MCQs on this topic.

Q1. What is the primary purpose of the BLAST tool in bioinformatics?

• Predicting 3D protein structure
• Searching sequence databases for local alignments
• Modeling pharmacokinetics
• Designing PCR primers

Correct Answer: Searching sequence databases for local alignments

Q2. Which file format commonly stores raw high-throughput sequencing reads with quality scores?

• PDB
• FASTA
• FASTQ
• SAM

Correct Answer: FASTQ

Q3. Which database is best known for curated protein sequences and functional annotations?

• GenBank
• UniProt/Swiss-Prot
• EMBL
• KEGG

Correct Answer: UniProt/Swiss-Prot

Q4. The Needleman–Wunsch algorithm is used for which task?

• Local sequence alignment
• Global sequence alignment
• Phylogenetic tree construction
• Protein docking simulation

Correct Answer: Global sequence alignment

Q5. Which substitution matrix is commonly used for protein alignments sensitive to evolutionary distance?

• PHRED
• BLOSUM
• FASTX
• GTF

Correct Answer: BLOSUM

Q6. What is the primary use of the Protein Data Bank (PDB) in pharmacy studies?

• Storing gene expression microarray data
• Providing experimentally determined 3D structures of biomolecules
• Hosting chemical compound patents
• Aligning nucleotide sequences

Correct Answer: Providing experimentally determined 3D structures of biomolecules

Q7. Which term describes computational prediction of a protein’s 3D structure using a homologous template?

• De novo folding
• Homology modeling
• Sequence assembly
• Microarray normalization

Correct Answer: Homology modeling

Q8. In NGS data analysis, what does SAM/BAM format store?

• Raw chromatogram peaks
• Aligned sequence reads and mapping information
• Protein interaction networks
• Metabolic pathway diagrams

Correct Answer: Aligned sequence reads and mapping information

Q9. Which bioinformatics approach is most useful for identifying conserved motifs across protein families?

• Phylogenetic profiling
• Motif discovery using position-specific scoring matrices or HMMs
• Metagenomic assembly
• Chromatography simulation

Correct Answer: Motif discovery using position-specific scoring matrices or HMMs

Q10. What does the term ‘ortholog’ refer to in comparative genomics?

• Genes related by duplication within the same species
• Genes in different species that evolved from a common ancestral gene by speciation
• Non-coding RNA sequences only found in bacteria
• Artificially synthesized genes

Correct Answer: Genes in different species that evolved from a common ancestral gene by speciation

Q11. Which tool is commonly used for multiple sequence alignment of proteins?

• Clustal Omega
• BWA
• Bowtie
• GATK

Correct Answer: Clustal Omega

Q12. Which database integrates genes, proteins, pathways, and drug information useful for pharmacology?

• RefSeq
• KEGG
• dbSNP
• FASTQ

Correct Answer: KEGG

Q13. In cheminformatics, QSAR models are used to predict which property?

• Sequence homology
• Drug activity or biological response from chemical structure
• Protein crystallization conditions
• RNA secondary structure

Correct Answer: Drug activity or biological response from chemical structure

Q14. What is the primary application of molecular docking in drug discovery?

• Predicting gene expression levels
• Estimating binding poses and affinities of small molecules to targets
• Assembling short sequencing reads
• Annotating genomes

Correct Answer: Estimating binding poses and affinities of small molecules to targets

Q15. Which resource would you use to find single nucleotide polymorphism (SNP) information?

• UniProt
• dbSNP
• PDB
• EMBL-EBI Clustal

Correct Answer: dbSNP

Q16. What does RNA-Seq measure that is particularly useful for pharmacogenomics?

• Protein tertiary structure
• Transcriptome expression levels and alternative splicing
• Metabolite concentrations
• Genomic copy number only

Correct Answer: Transcriptome expression levels and alternative splicing

Q17. Which algorithm is used for optimal local alignment between two sequences?

• Needleman–Wunsch
• Smith–Waterman
• ClustalW
• FastQC

Correct Answer: Smith–Waterman

Q18. What is the role of Gene Ontology (GO) annotations in bioinformatics?

• Providing 3D structural coordinates
• Standardizing descriptions of gene products’ functions, processes, and components
• Storing raw sequencing reads
• Designing chemical synthesis routes

Correct Answer: Standardizing descriptions of gene products’ functions, processes, and components

Q19. Which technique is essential for assembling short reads into longer contiguous sequences (contigs)?

• Genome annotation
• De novo sequence assembly
• Protein-ligand docking
• Phylogenetic profiling

Correct Answer: De novo sequence assembly

Q20. Which of the following is a common use of phylogenetic analysis in pharmaceutical research?

• Predicting drug solubility
• Tracing evolutionary relationships of pathogens and resistance genes
• Measuring blood-brain barrier permeability
• Designing drug formulation excipients

Correct Answer: Tracing evolutionary relationships of pathogens and resistance genes

Q21. What does ADMET prediction in silico aim to estimate?

• Sequence alignment scores
• Absorption, Distribution, Metabolism, Excretion, and Toxicity of compounds
• Protein secondary structure
• Genome assembly quality

Correct Answer: Absorption, Distribution, Metabolism, Excretion, and Toxicity of compounds

Q22. Which format is typically used to represent protein or nucleotide sequences for BLAST and alignments?

• SAM
• FASTA
• BED
• GFF

Correct Answer: FASTA

Q23. Which machine learning approach is often applied in bioinformatics for classification of compounds or gene expression patterns?

• Homology modeling
• Support Vector Machines (SVM) or Random Forests
• Smith–Waterman algorithm
• Needleman–Wunsch algorithm

Correct Answer: Support Vector Machines (SVM) or Random Forests

Q24. What is the significance of BLOSUM matrices in sequence analysis?

• They provide quality scores for sequencing reads
• They offer substitution scores derived from conserved blocks for protein alignment
• They are used to store 3D coordinates
• They annotate gene ontology terms

Correct Answer: They offer substitution scores derived from conserved blocks for protein alignment

Q25. Which resource is most suitable for pathway enrichment analysis of a gene list?

• FastQC
• KEGG or Reactome
• PDB
• FASTQ

Correct Answer: KEGG or Reactome

Q26. In structural bioinformatics, RMSD is used to measure what?

• Sequence read depth
• Root mean square deviation between atomic positions of structures
• GC content of a genome
• Quality trimming threshold

Correct Answer: Root mean square deviation between atomic positions of structures

Q27. Which of these tools is commonly used for quality control of raw NGS reads?

• FastQC
• AutoDock Vina
• Clustal
• PhyML

Correct Answer: FastQC

Q28. Which database specializes in pathways and molecular interactions relevant to drug targets?

• UniProt
• DrugBank
• RefSeq
• GEO

Correct Answer: DrugBank

Q29. Hidden Markov Models (HMMs) are particularly useful in bioinformatics for:

• Modeling protein family profiles and detecting remote homologs
• Visualizing 3D protein structures
• Sequencing DNA fragments
• Predicting ADMET properties

Correct Answer: Modeling protein family profiles and detecting remote homologs

Q30. How does comparative genomics contribute to identifying potential drug targets?

• By simulating drug metabolism in silico only
• By comparing genomes to find conserved essential genes and pathogen-specific pathways
• By predicting protein tertiary structure from scratch
• By measuring chromatographic retention times

Correct Answer: By comparing genomes to find conserved essential genes and pathogen-specific pathways

G S Sachin

I am a Registered Pharmacist under the Pharmacy Act, 1948, and the founder of PharmacyFreak.com. I hold a Bachelor of Pharmacy degree from Rungta College of Pharmaceutical Science and Research. With a strong academic foundation and practical knowledge, I am committed to providing accurate, easy-to-understand content to support pharmacy students and professionals. My aim is to make complex pharmaceutical concepts accessible and useful for real-world application.

Mail- Sachin@pharmacyfreak.com