Concepts and scope of Bioinformatics MCQs With Answer

Concepts and scope of Bioinformatics MCQs With Answer introduce B. Pharm students to essential computational approaches used in modern pharmaceutical research. This concise, keyword-rich overview explains core concepts—sequence analysis, databases (GenBank, UniProt, PDB), genomics, proteomics, pharmacogenomics, molecular docking, cheminformatics and data mining—plus practical tools such as BLAST, Clustal and HMM-based searches. Understanding the scope includes applications in drug discovery, target identification, ADMET prediction and translational research. Emphasis on interpretation of results, quality control in NGS and functional annotation prepares pharmacy graduates for interdisciplinary work. These MCQs reinforce conceptual clarity and exam readiness while linking theory to real-world bioinformatics workflows. Now let’s test your knowledge with 30 MCQs on this topic.

Q1. What is the primary definition of bioinformatics in a pharmaceutical context?

• Integration of biology, computer science and statistics to analyze biological data for drug discovery
• Exclusive laboratory techniques for drug formulation
• Clinical trial management and patient recruitment
• Manufacturing processes for pharmaceutical production

Correct Answer: Integration of biology, computer science and statistics to analyze biological data for drug discovery

Q2. Which database is the principal public repository for nucleotide sequence data?

• UniProt
• GenBank
• PDB
• KEGG

Correct Answer: GenBank

Q3. Which resource contains manually curated, reviewed protein sequence entries valuable for B. Pharm students?

• TrEMBL
• UniProtKB/Swiss-Prot
• GenBank nucleotide
• PubChem

Correct Answer: UniProtKB/Swiss-Prot

Q4. What is the main purpose of the BLAST algorithm?

• Find regions of local similarity between sequences
• Perform whole-genome assembly
• Model 3D protein structures from scratch
• Predict ADMET properties of small molecules

Correct Answer: Find regions of local similarity between sequences

Q5. Which algorithm is used for global pairwise sequence alignment?

• Smith-Waterman
• Needleman-Wunsch
• BLAST
• HMMER

Correct Answer: Needleman-Wunsch

Q6. Which scoring matrix is commonly used for protein sequence alignments based on observed substitutions?

• PHRED
• BLOSUM
• PAM only for nucleotides
• FastQC

Correct Answer: BLOSUM

Q7. In BLAST output, the e-value represents:

• The expected number of alignments with this score that could occur by chance
• The exact evolutionary distance between two species
• The molecular weight of the protein
• The percentage GC content of the sequence

Correct Answer: The expected number of alignments with this score that could occur by chance

Q8. The Protein Data Bank (PDB) is primarily used to store:

• Gene expression microarray data
• 3D structures of proteins and nucleic acids
• Small-molecule drug sales data
• Clinical trial outcomes

Correct Answer: 3D structures of proteins and nucleic acids

Q9. Hidden Markov Models (HMMs) in bioinformatics are especially useful for:

• Predicting chromatographic retention times
• Modeling sequence families and detecting domains
• Simulating pharmacokinetic time courses
• Counting reads in a FASTQ file

Correct Answer: Modeling sequence families and detecting domains

Q10. An open reading frame (ORF) is defined as:

• A region of DNA between two promoters
• A continuous stretch of codons from a start codon to a stop codon
• A noncoding intronic region
• A domain within a protein structure

Correct Answer: A continuous stretch of codons from a start codon to a stop codon

Q11. Next-generation sequencing (NGS) technologies typically generate:

• Large volumes of short reads for high-throughput analysis
• Single high-quality long reads only
• Protein 3D structures directly
• Pharmacokinetic profiles

Correct Answer: Large volumes of short reads for high-throughput analysis

Q12. The FASTQ file format contains:

• Only nucleotide sequences without quality scores
• Only quality scores without sequences
• Sequence records with per-base quality scores
• 3D coordinates for atoms

Correct Answer: Sequence records with per-base quality scores

Q13. Which tool is commonly used for multiple sequence alignment of protein or nucleotide sequences?

• ClustalW
• FASTQC
• Bowtie
• AutoDock

Correct Answer: ClustalW

Q14. KEGG is a database primarily used for:

• Protein 3D structure deposition
• Pathway mapping and metabolic networks
• Nucleotide sequence archiving
• Clinical trial registration

Correct Answer: Pathway mapping and metabolic networks

Q15. The Swiss-Prot section of UniProt is characterized by:

• Automatically annotated, unreviewed entries
• Reviewed, manually annotated protein entries
• Only nucleotide sequences
• Pharmaceutical sales data

Correct Answer: Reviewed, manually annotated protein entries

Q16. Homology (comparative) modeling of a protein requires:

• A chemical synthesis protocol for the protein
• An experimentally solved template structure from PDB
• Only the mRNA expression profile
• Clinical pharmacology data

Correct Answer: An experimentally solved template structure from PDB

Q17. Molecular docking in drug discovery is used to:

• Predict ligand binding orientation and estimate binding affinity to a target
• Sequence genomes rapidly
• Annotate gene function automatically
• Measure blood concentration in patients

Correct Answer: Predict ligand binding orientation and estimate binding affinity to a target

Q18. In cheminformatics, SMILES is a format used to represent:

• Protein secondary structure
• Small-molecule chemical structures as linear strings
• Genome assembly graphs
• LC-MS chromatograms

Correct Answer: Small-molecule chemical structures as linear strings

Q19. Pharmacogenomics primarily studies the relationship between:

• Drug prices and market demand
• Genetic variation and individual drug response
• Environmental toxins and crop yield
• Protein folding dynamics only

Correct Answer: Genetic variation and individual drug response

Q20. A SNP (single nucleotide polymorphism) is best described as:

• A type of copy number variation affecting many bases
• A single-base change at a specific position in the genome that occurs commonly in a population
• A large chromosomal translocation event
• An epigenetic methylation mark

Correct Answer: A single-base change at a specific position in the genome that occurs commonly in a population

Q21. Functional annotation of a gene sequence involves:

• Predicting its biological role, domains and pathway associations
• Measuring its solubility in water
• Sequencing the entire chromosome manually
• Calculating drug half-life in vivo

Correct Answer: Predicting its biological role, domains and pathway associations

Q22. In genome assembly terminology, a contig is:

• An ordered set of scaffolds linked by gaps
• A continuous consensus sequence assembled from overlapping reads
• A type of protein domain
• A sequencing platform

Correct Answer: A continuous consensus sequence assembled from overlapping reads

Q23. Compared to microarrays, RNA-seq provides:

• Lower sensitivity for low-abundance transcripts
• Sequence-based, digital quantification with higher dynamic range
• Only predefined probes for known genes
• Protein expression levels directly

Correct Answer: Sequence-based, digital quantification with higher dynamic range

Q24. In BLAST results, the bit score represents:

• The raw alignment score without normalization
• A normalized score allowing comparisons across different searches
• The mass-to-charge ratio of peptides
• The GC content of the query

Correct Answer: A normalized score allowing comparisons across different searches

Q25. The Smith-Waterman algorithm is used for:

• Local sequence alignment to find the best matching subregions
• Molecular dynamics simulation of proteins
• Predicting pharmacokinetic parameters
• Global alignment of whole genomes only

Correct Answer: Local sequence alignment to find the best matching subregions

Q26. BLOSUM matrices are derived from:

• Simulated mutation rates only
• Observed substitutions in conserved blocks of aligned protein sequences
• Quality scores from sequencing reads
• X-ray crystallography B-factors

Correct Answer: Observed substitutions in conserved blocks of aligned protein sequences

Q27. NCBI Entrez is best described as:

• A standalone genome assembler
• An integrated retrieval system for multiple NCBI databases
• A molecular docking engine
• A clinical data repository for hospitals

Correct Answer: An integrated retrieval system for multiple NCBI databases

Q28. Which task is least associated with structural bioinformatics?

• Predicting the 3D fold of a protein
• Analyzing protein–ligand interactions
• Comparative modeling using templates
• Predicting population-level adverse drug reaction frequencies

Correct Answer: Predicting population-level adverse drug reaction frequencies

Q29. Which database specializes in protein families represented by HMM profiles?

• CATH
• SCOP
• Pfam
• PDB

Correct Answer: Pfam

Q30. In genome assembly evaluation, the N50 metric indicates:

• The number of contigs in the assembly
• The length such that 50% of the assembly is contained in contigs of that length or longer
• The average GC content of the largest scaffolds
• The quality score threshold for read trimming

Correct Answer: The length such that 50% of the assembly is contained in contigs of that length or longer

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