Introduction to bioinformatics MCQs With Answer

Introduction: Introduction to bioinformatics MCQs With Answer is designed for M.Pharm students to build a solid foundation in computational methods applied to pharmaceutical and biological research. This set of carefully crafted multiple-choice questions focuses on core concepts such as sequence databases, alignment algorithms, scoring matrices, genome annotation, structure prediction, and applications in pharmacogenomics and drug discovery. Each question includes concise answer choices and clear, bolded correct responses to aid rapid revision. The quiz balances conceptual understanding with practical interpretation of bioinformatics outputs, preparing students to interpret sequence analysis, identify functional motifs, and apply computational tools to real-world pharmaceutical problems.

Q1. What is the primary objective of bioinformatics in pharmaceutical research?

• To replace laboratory experiments entirely with computer simulations
• To apply computational and statistical techniques to analyze biological data for discovery and decision-making
• To design laboratory equipment for high-throughput screening
• To develop new chemical synthesis pathways for drug manufacturing

Correct Answer: To apply computational and statistical techniques to analyze biological data for discovery and decision-making

Q2. Which data format is most commonly used to represent nucleotide or protein sequences in plain text?

• GenBank flat file
• FASTQ
• FASTA
• PDB

Correct Answer: FASTA

Q3. The basic local alignment search tool (BLAST) primarily reports which of the following to indicate the statistical significance of a sequence match?

• GC content
• Melting temperature
• E-value
• Identity percentage only

Correct Answer: E-value

Q4. Which substitution matrix is most appropriate for aligning closely related protein sequences?

• BLOSUM45
• Identity matrix
• BLOSUM80
• PAM250

Correct Answer: BLOSUM80

Q5. In pairwise sequence alignment, what is the main difference between global and local alignment?

• Global alignment finds the best matching subsequence; local alignment aligns entire sequences end-to-end
• Global alignment aligns entire sequences end-to-end; local alignment finds the best matching subsequence
• Global uses scoring matrices; local does not
• There is no difference; they are synonyms

Correct Answer: Global alignment aligns entire sequences end-to-end; local alignment finds the best matching subsequence

Q6. Which public database is the primary repository for experimentally determined 3D structures of proteins and nucleic acids?

• UniProt
• GenBank
• PDB (Protein Data Bank)
• KEGG

Correct Answer: PDB (Protein Data Bank)

Q7. In genome annotation, an Open Reading Frame (ORF) is defined as:

• A non-coding RNA predicted by structural motifs
• A DNA segment between a start codon and a stop codon that could be translated into a protein
• The promoter region upstream of a gene
• A conserved protein domain detected by HMM

Correct Answer: A DNA segment between a start codon and a stop codon that could be translated into a protein

Q8. Hidden Markov Models (HMMs) are widely used in bioinformatics for which purpose?

• Predicting ligand-binding affinities in docking
• Modeling and detecting conserved sequence families and motifs
• Simulating molecular dynamics of proteins
• Generating synthetic DNA sequences for cloning

Correct Answer: Modeling and detecting conserved sequence families and motifs

Q9. Which method is most appropriate for predicting the 3D structure of a protein when a close homolog with known structure exists?

• Ab initio (de novo) modeling
• Homology (comparative) modeling
• Molecular dynamics without templates
• Random coil approximation

Correct Answer: Homology (comparative) modeling

Q10. In BLAST output, what does a low E-value indicate?

• The match is likely due to random chance
• The sequences are too short to compare
• The alignment is statistically significant and unlikely to be due to chance
• There is low alignment identity

Correct Answer: The alignment is statistically significant and unlikely to be due to chance

Q11. Which resource provides curated protein sequence and functional information commonly used in drug target research?

• Swiss-Prot section of UniProt
• BLAST local databases
• Raw SRA reads
• RefSeq bacterial genomes only

Correct Answer: Swiss-Prot section of UniProt

Q12. What is a primary application of multiple sequence alignment (MSA) in pharmaceutical bioinformatics?

• Quantifying metabolite concentrations
• Identifying conserved residues and functional motifs for target validation
• Directly predicting drug toxicity without experiments
• Sequencing genomes faster

Correct Answer: Identifying conserved residues and functional motifs for target validation

Q13. Which high-throughput technology produces short sequencing reads used for transcriptome profiling and variant discovery?

• First-generation Sanger sequencing
• Next-generation sequencing (NGS)
• Mass spectrometry proteomics
• Southern blotting

Correct Answer: Next-generation sequencing (NGS)

Q14. In pharmacogenomics, which type of genetic variation is most often associated with individual responses to drugs?

• Chromosomal translocations only
• Single nucleotide polymorphisms (SNPs)
• Large mitochondrial genome rearrangements
• Transient RNA modifications

Correct Answer: Single nucleotide polymorphisms (SNPs)

Q15. Which tool or algorithm is commonly used to search sequence databases for local similarity to a query nucleotide or protein?

• ClustalW
• BLAST
• Phyre2
• ROSETTA

Correct Answer: BLAST

Q16. Gene Ontology (GO) annotations describe gene products in terms of which three domains?

• Expression level, chromosomal location, and sequence length
• Biological process, molecular function, and cellular component
• Pathway ID, enzyme commission number, and pI value
• Transcript isoform count, GC content, and codon usage

Correct Answer: Biological process, molecular function, and cellular component

Q17. What does a high bit score in a sequence alignment indicate?

• Poor alignment quality
• High confidence and better quality alignment independent of database size
• Only longer sequences can get high bit scores
• Higher mutation rate in the sequence

Correct Answer: High confidence and better quality alignment independent of database size

Q18. Which database is specifically tailored for pathways and enzyme-centric maps useful in drug metabolism studies?

• PubMed
• KEGG (Kyoto Encyclopedia of Genes and Genomes)
• ClinVar
• dbSNP

Correct Answer: KEGG (Kyoto Encyclopedia of Genes and Genomes)

Q19. What is the main goal of molecular docking in computational drug discovery?

• To sequence the genome of drug targets
• To predict the preferred orientation and interaction of a small molecule with a target binding site
• To increase the metabolic stability of a compound in silico without experiments
• To align multiple protein sequences

Correct Answer: To predict the preferred orientation and interaction of a small molecule with a target binding site

Q20. In transcriptomics, differential expression analysis aims to identify genes that:

• Have identical expression across all samples
• Are present only in the genome but not transcribed
• Show statistically significant changes in expression between conditions or treatments
• Contain the highest number of exons

Correct Answer: Show statistically significant changes in expression between conditions or treatments

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