Bioinformatics MCQs

1. Which of the following algorithms is primarily used for sequence alignment in bioinformatics?
(A) Smith-Waterman
(B) K-means clustering
(C) Random Forest
(D) Euclidean distance

2. Which of the following tools is used for multiple sequence alignment?
(A) BLAST
(B) ClustalW
(C) FASTA
(D) Biopython

3. In bioinformatics, what does the term “BLAST” stand for?
(A) Basic Local Alignment Search Tool
(B) Bioinformatics Local Algorithmic Search Tool
(C) Basic Linear Alignment Search Tool
(D) Biometric Linear Alignment Search Tool

4. Which of the following represents the process of converting raw sequencing data into usable information?
(A) Sequence assembly
(B) Data mining
(C) Machine learning
(D) Data preprocessing

5. What does the E-value represent in a BLAST search?
(A) The total number of sequences in the database
(B) The expected number of times the alignment could occur by chance
(C) The quality score of the alignment
(D) The similarity percentage of two sequences

6. Which of the following is a key feature of high-throughput sequencing technologies?
(A) They only sequence a single gene
(B) They can sequence millions of DNA molecules in parallel
(C) They require large amounts of DNA
(D) They do not generate raw data

7. What is the main purpose of protein structure prediction in bioinformatics?
(A) To determine the amino acid sequence of a protein
(B) To determine the 3D structure of a protein from its amino acid sequence
(C) To calculate the number of genes in a genome
(D) To quantify the number of proteins expressed in a cell

8. What is the purpose of a phylogenetic tree in bioinformatics?
(A) To predict the function of a protein
(B) To classify sequences based on similarity
(C) To map a genome to a reference sequence
(D) To show the evolutionary relationships between sequences

9. Which of the following algorithms is used to detect conserved motifs in biological sequences?
(A) BLAST
(B) HMMER
(C) Needleman-Wunsch
(D) ClustalW

10. In next-generation sequencing (NGS), what is the purpose of a “read”?
(A) A short segment of RNA that binds to a template
(B) A segment of DNA generated during the sequencing process
(C) A unique identifier for each sequencing experiment
(D) A data file containing raw sequencing results

11. Which of the following file formats is commonly used to store sequence data in bioinformatics?
(A) PDF
(B) FASTA
(C) TXT
(D) CSV

12. What is the main challenge addressed by the “de novo” genome assembly method in bioinformatics?
(A) Aligning sequences to a known reference genome
(B) Assembling a genome without a pre-existing reference
(C) Determining the amino acid sequence of proteins
(D) Identifying genes and their functions

13. Which bioinformatics tool is used for detecting gene expression levels from RNA-seq data?
(A) BLAST
(B) TopHat
(C) PhyML
(D) GenBank

14. Which of the following describes a major advantage of using a sequence alignment tool like ClustalW or MUSCLE?
(A) They provide evolutionary analysis of proteins
(B) They can handle millions of sequences at once
(C) They align multiple sequences to identify conserved regions
(D) They predict the function of a gene

15. Which of the following is NOT a type of data generated by bioinformatics tools in genomic studies?
(A) Sequence alignments
(B) Genome-wide association studies (GWAS) results
(C) Protein folding prediction
(D) Clustering of expression data