BIN-422 – Introduction to Bioinformatics 1. Who coined the term "bioinformatics"? A) Linus Pauling B) Paulien Hogeweg C) Watson D) Francis Crick Answer: B 2. Bioinformatics is a combination of biology and: A) Physics B) Chemistry C) Computer Science D) Mathematics Answer: C 3. What is the primary aim of bioinformatics? A) DNA sequencing B) Protein production C) Data storage and analysis D) Drug delivery Answer: C 4. Which of the following is a key application of bioinformatics? A) Drug discovery B) Genome analysis C) Disease diagnosis D) All of the above Answer: D 5. Which field does NOT contribute directly to bioinformatics? A) Genetics B) Computer Programming C) Sociology D) Statistics Answer: C 6. The central biological molecule studied in bioinformatics is: A) Carbohydrate B) DNA C) Lipid D) Hormone Answer: B 7. Which software is commonly used for 3D protein structure prediction? A) MS Excel B) Photoshop C) SWISS-MODEL D) Windows Media Player Answer: C 8. Which of the following is considered an omics science? A) Astronomy B) Proteomics C) Engineering D) Optics Answer: B 9. When was the Human Genome Project completed? A) 2001 B) 2003 C) 2005 D) 2010 Answer: B 10. Which of the following is NOT an application of bioinformatics? A) Studying evolution B) Agricultural improvement 11. What is the full form of NCBI? A) National Center for Biotechnology Interface B) National Centre for Biological Inventions C) National Center for Biotechnology Information D) National Cell Biology Institute Answer: C 12. Which database stores nucleotide sequences? A) PDB B) GenBank C) UniProt D) SWISS-PROT Answer: B 13. What type of data does UniProt database contain? A) Protein sequences B) DNA sequences C) RNA sequences D) Metabolic pathways Answer: A 14. EMBL database is maintained by which organization? A) USA B) Japan C) Europe D) Australia Answer: C 15. DDBJ stands for: A) DNA Data Bank of Japan B) Database of DNA of Japan C) Data Deposit Bank of Japan D) DNA Data Bureau of Japan Answer: A 16. BLAST stands for: A) Basic Local Alignment Search Tool B) Binary Local Alignment Search Tool C) Basic Linear Alignment Search Tool D) Bioinformatics Local Analysis Search Tool Answer: A 17. What does BLAST do? A) Predicts protein 3D structure B) Aligns sequences to find similarities C) Annotates genomes D) Stores metabolic data Answer: B 18. Which algorithm does BLAST use? A) Heuristic B) Dynamic Programming C) Machine Learning D) Greedy Answer: A 19. Which tool is used for multiple sequence alignment? A) BLAST B) ClustalW C) FASTA D) RASMOL Answer: B 20. What is the main difference between global and local alignment? A) Global aligns whole sequences, local aligns subsequences B) Local aligns whole sequences, global aligns subsequences C) Global is faster than local D) Local is used for proteins only Answer: A 21. The FASTA format contains: A) Protein 3D structure B) Sequence data with a description line C) Metabolic pathway maps D) Phylogenetic trees Answer: B 22. Which tool predicts gene locations in DNA sequences? A) GenScan B) BLAST C) ClustalW D) SWISS-MODEL Answer: A 23. What is genome annotation? A) Sequencing the genome B) Identifying genes and their functions C) Storing sequences in databases D) Protein folding analysis Answer: B 24. What is phylogenetic analysis used for? A) Predicting genes B) Studying evolutionary relationships C) Analyzing protein folding D) Genome assembly Answer: B 25. Which type of tree represents evolutionary relationships? A) Binary tree B) Phylogenetic tree C) Decision tree D) Random tree Answer: B 26. What is the main principle behind protein structure prediction? A) Sequence homology B) DNA methylation C) RNA transcription D) Metabolic pathway Answer: A 27. Which tool is commonly used for protein structure visualization? A) RASMOL B) BLAST C) GenBank D) EMBL Answer: A 28. What is a biological database? A) Software for sequence alignment B) Collection of biological data organized for retrieval C) Protein folding algorithm D) Visualization software Answer: B 29. Which database specializes in protein sequences? A) GenBank B) UniProt C) EMBL D) DDBJ Answer: B 30. What is the role of bioinformatics in drug discovery? A) Identifying potential drug targets B) Synthesizing drugs C) Marketing drugs D) Packaging drugs Answer: A 31. Which is NOT a type of biological database? A) Primary B) Secondary C) Tertiary D) Physical Answer: D 32. Which of the following is an example of a secondary database? A) GenBank B) Pfam C) DDBJ D) EMBL Answer: B 33. What is the use of Pfam database? A) Protein families classification B) DNA sequencing C) Gene prediction D) Metabolic pathways Answer: A 34. Which one is NOT a nucleotide database? A) GenBank B) EMBL C) UniProt D) DDBJ Answer: C 35. Which format is widely used for representing sequence alignments? A) FASTA B) GenBank C) Clustal D) PDB Answer: C 36. Which technique is used in structural bioinformatics? A) X-ray crystallography data analysis B) Metabolic profiling C) RNA transcription D) DNA sequencing Answer: A 37. What is the major output of BLAST? A) List of similar sequences with scores B) 3D protein structure C) Genome annotation D) Phylogenetic tree Answer: A 38. What is the purpose of multiple sequence alignment? A) Predict protein folding B) Identify conserved regions among sequences C) Sequence assembly D) Gene expression analysis Answer: B 39. Which database provides 3D structures of proteins? A) PDB B) GenBank C) UniProt D) EMBL Answer: A 40. What is the smallest unit of information stored in databases? A) Sequence B) Gene C) Nucleotide D) Protein Answer: C 41. What is FASTQ format used for? A) Storing raw sequence data with quality scores B) Protein structure C) Metabolic pathways D) Phylogenetic trees Answer: A 42. Which of the following is NOT a step in genome annotation? A) Gene prediction B) Functional annotation C) DNA sequencing D) Protein structure prediction Answer: C 43. The Needleman-Wunsch algorithm is used for: A) Global sequence alignment B) Local sequence alignment C) Genome assembly D) Phylogenetic analysis Answer: A 44. The Smith-Waterman algorithm is used for: A) Global sequence alignment B) Local sequence alignment C) Gene prediction D) Protein folding Answer: B 45. What is a 'motif' in bioinformatics? A) A recurring sequence pattern with biological significance B) Protein folding pattern C) Database format D) Visualization technique Answer: A 46. Which is a common format for 3D protein structures? A) FASTA B) PDB C) GenBank D) EMBL Answer: B 47. What is an ortholog? A) Gene in the same species with similar function B) Genes in different species evolved from a common ancestor C) A protein folding pattern D) A database entry Answer: B 48. What is the use of the tool Clustal Omega? A) Sequence alignment B) Protein structure prediction C) Gene expression analysis D) Drug design Answer: A 49. Which is NOT a characteristic of a good bioinformatics database? A) Accuracy B) Completeness C) Security D) Unreadability Answer: D 50. What is a contig? A) Overlapping DNA sequences that form a consensus region B) Protein domain C) RNA transcript D) Metabolic pathway Answer: A 51. What is transcriptomics? A) Study of all RNA transcripts B) Study of proteins C) Study of DNA sequences D) Study of metabolism Answer: A 52. Which database is used for storing gene expression data? A) GEO B) GenBank C) PDB D) UniProt Answer: A 53. Which tool is used for gene expression analysis? A) BLAST B) GEO2R C) ClustalW D) GenScan Answer: B 54. What is the role of bioinformatics in personalized medicine? A) Tailoring treatment based on genetic information B) Manufacturing drugs C) Hospital management D) Medical imaging Answer: A 55. Which of these is NOT a sequence alignment tool? A) BLAST B) FASTA C) ClustalW D) Photoshop Answer: D 56. What is the significance of a 'gap' in sequence alignment? A) Insertions or deletions in sequences B) Protein folding region C) Database error D) Gene mutation Answer: A 57. What is the difference between DNA and RNA sequences? A) DNA contains uracil, RNA contains thymine B) DNA is double-stranded, RNA single-stranded C) DNA has ribose sugar, RNA has deoxyribose D) DNA is a protein, RNA is lipid Answer: B 58. Which of the following is a limitation of bioinformatics? A) Large data handling B) Experimental verification still needed C) Automation D) High speed of analysis Answer: B 59. Which type of mutation can bioinformatics help detect? A) Point mutation B) Frame-shift mutation C) Both A and B D) None of these Answer: C 60. What is the main purpose of gene ontology (GO)? A) Classify gene functions B) Sequence alignment C) Protein structure prediction D) Drug discovery Answer: A