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Question 1. Which file format stores nucleotide sequences with associated quality scores? A) FASTA B) FASTQ C) GFF D) SAM Answer: B Explanation: FASTQ combines the sequence (FASTA style) with per-base quality scores, essential for NGS data. Question 2. In the central dogma, which process converts RNA into protein? A) Transcription B) Replication C) Translation D) Splicing Answer: C Explanation: Translation reads mRNA codons to synthesize a polypeptide chain. Question 3. What does the ‘N’ nucleotide code represent in a FASTA file? A) Adenine B) Cytosine C) Any nucleotide (A, C, G, or T) D) Gap Answer: C Explanation: ‘N’ denotes an ambiguous base where the exact nucleotide is unknown. Question 4. Which substitution matrix is most appropriate for comparing highly divergent protein sequences? A) BLOSUM
B) BLOSUM
C) PAM
D) PAM
Answer: C Explanation: PAM250 is derived from highly divergent sequences, making it suitable for distant comparisons. Question 5. The Needleman-Wunsch algorithm is used for: A) Local alignment of short motifs B) Global alignment of entire sequences C) Database searching with heuristics D) Phylogenetic tree construction Answer: B Explanation: Needleman-Wunsch performs optimal global alignment across the full length of two sequences. Question 6. Which BLAST variant aligns a protein query against a nucleotide database translated in all six frames? A) BLASTn B) BLASTp C tBLASTn D) BLASTx Answer: C Explanation: tBLASTn uses a protein query against a translated nucleotide database. Question 7. In a phylogenetic tree, a node that represents the most recent common ancestor of a group of taxa is called a: A) Leaf B) Clade C) Root
Explanation: An ORF is a continuous codon series that begins with a start codon and ends at a stop codon without interruptions. Question 11. The UniProtKB database primarily provides information about: A) Nucleotide sequences B) Protein sequences and functional annotation C) Metabolic pathways D) Gene expression profiles Answer: B Explanation: UniProtKB curates protein sequences, domains, functions, and post-translational modifications. Question 12. In a hydropathy plot, a region with a high positive score most likely corresponds to: A) A transmembrane helix B) A signal peptide cleavage site C) A nuclear localization signal D) A low-complexity region Answer: A Explanation: Positive hydropathy values indicate hydrophobic residues typical of membrane-spanning segments. Question 13. Which of the following is a gap penalty type used in alignment scoring? A) Linear penalty only B) Affine penalty (gap open + gap extend) C) Exponential penalty D) No penalty is ever applied Answer: B Explanation: Affine penalties assign a higher cost for opening a gap and a lower cost for extending it, reflecting biological reality.
Question 14. The basic command to extract all sequences matching “>geneX” from a FASTA file using grep is: A) grep “geneX” file.fasta B) grep -A 1 “>geneX” file.fasta C) grep -B 1 “geneX” file.fasta D) grep -C 1 “>geneX” file.fasta Answer: B Explanation: -A 1 prints the matching header line and the following sequence line. Question 15. Which distance-based method assumes a constant rate of evolution (molecular clock) across lineages? A) Neighbor-Joining B) UPGMA C) Maximum Likelihood D) Bayesian Inference Answer: B Explanation: UPGMA clusters taxa assuming equal evolutionary rates, producing an ultrametric tree. Question 16. In the context of LBC tools, which analysis is considered “low-complexity”? A) Whole-genome assembly B) Single-gene BLAST search C) Metagenomic binning D) De-novo transcriptome reconstruction Answer: B Explanation: LBC focuses on simple, single-gene or short-sequence tasks rather than large-scale analyses. Question 17. Which of the following amino-acid one-letter codes represents Lysine?
D) A gap-rich region Answer: B Explanation: Conservation suggests evolutionary pressure to maintain that residue’s function. Question 21. Which command would you use to view the first 10 lines of a FASTA file? A) tail -n 10 file.fasta B) head -n 10 file.fasta C) less file.fasta D) cat file.fasta | grep “>” Answer: B Explanation: head prints the beginning of a file; -n 10 limits output to ten lines. Question 22. The BLOSUM62 matrix was derived from sequences with what level of similarity? A) 62 % identical over the alignment window B) 62 % divergent C) 30 % identical D) 250 % similarity Answer: A Explanation: BLOSUM62 is built from blocks of sequences sharing no more than 62 % identity, making it suitable for moderate similarity searches. Question 23. Which of the following best defines a “rooted” phylogenetic tree? A) A tree without a designated ancestor B) A tree with a branch that represents the most recent common ancestor of all taxa C) A tree that displays only pairwise distances D) A tree that cannot be rerooted Answer: B
Explanation: A rooted tree includes an explicit outgroup or root, indicating direction of evolution. Question 24. When translating a DNA sequence, which codon signals the start of translation? A) UGA B) UAA C) AUG D) UGG Answer: C Explanation: AUG codes for Methionine and serves as the canonical start codon in most organisms. Question 25. In a FASTA header, the accession number is typically found after which character? A) ‘|’ B) ‘>’ C) ‘#’ D) ‘$’ Answer: B Explanation: FASTA headers begin with ‘>’, followed by an identifier such as an accession number. Question 26. Which of the following tools is primarily used for building a phylogenetic tree from a distance matrix? A) MUSCLE B) ClustalW C) PHYLIP’s neighbor D) BLASTp Answer: C Explanation: PHYLIP’s neighbor program implements the Neighbor-Joining algorithm using a distance matrix.
B) You want to find a conserved domain within larger, divergent sequences. C) You need to compute phylogenetic distances. D) You are assembling a genome. Answer: B Explanation: Local alignment (Smith-Waterman) isolates the best matching region, ideal for detecting domains. Question 31. The command grep -c “>” file.fasta returns: A) The total number of characters in the file B) The number of sequence lines C) The number of FASTA headers (i.e., sequences) D) The number of gaps in the alignment Answer: C Explanation: -c counts matching lines; ‘>’ marks each header line. Question 32. Which of the following is NOT a typical component of a GenBank record? A) LOCUS line B) FEATURES table C) ORIGIN sequence block D) FASTQ quality scores Answer: D Explanation: GenBank stores nucleotide sequences (FASTA style) but does not include FASTQ quality data. Question 33. In sequence alignment scoring, a “match” typically receives a: A) Negative score B) Zero score C) Positive score D) Random score Answer: C
Explanation: Matches are rewarded with positive scores to favor aligned identical residues. Question 34. Which of the following is a valid reason to use the “tBLASTx” program? A) To compare a nucleotide query against a protein database B) To compare a protein query against a nucleotide database (translated) C) To compare a nucleotide query translated in all six frames against a protein database translated in all six frames D) To compare a protein query against a protein database Answer: C Explanation: tBLASTx translates both query and database nucleotides in all six frames before protein-protein comparison. Question 35. The term “pI” for a protein refers to: A) The isoelectric point where the protein has net zero charge B) The precipitation index C) The protein interaction score D) The predicted immunogenicity Answer: A Explanation: pI is the pH at which a protein’s overall charge is neutral. Question 36. Which of the following best describes the “gap open penalty” in alignment algorithms? A) The score subtracted for each gap extension B) The cost applied once when a new gap begins C) The reward for aligning gaps with gaps D) The penalty for mismatches only Answer: B Explanation: Gap open penalty is incurred when a gap is first introduced; subsequent extensions incur a separate (usually smaller) penalty.
B) cat file1.fasta file2.fasta > combined.fasta C) merge file1.fasta file2.fasta > combined.fasta D) combine file1.fasta file2.fasta > combined.fasta Answer: B Explanation: cat lists the contents of both files and redirects them into a new file. Question 41. In a substitution matrix, a high positive score for a pair of amino acids indicates: A) Frequent substitution in evolution B) Rare substitution in evolution C) No evolutionary information D) The pair is never observed together Answer: A Explanation: Positive scores reflect favorable or common substitutions observed in related proteins. Question 42. Which of the following is true about the “Smith-Waterman” algorithm? A) It always produces a global alignment. B) It uses a heuristic approach to speed up searches. C) It finds the optimal local alignment between two sequences. D) It cannot handle gaps. Answer: C Explanation: Smith-Waterman exactly computes the highest-scoring local alignment, including gaps. Question 43. The “grep” command is most useful for: A) Sorting sequences alphabetically B) Counting the number of nucleotides C) Searching for specific patterns in text files D) Translating DNA to protein
Answer: C Explanation: grep searches for regular-expression patterns within files. Question 44. Which of the following best describes a “clade” in a phylogenetic tree? A) Any leaf node B) A group consisting of a common ancestor and all its descendants C) The longest branch in the tree D) The root of the tree Answer: B Explanation: A clade is a monophyletic group defined by a single ancestor and all of its lineages. Question 45. In a basic LBC workflow, which step would most likely involve the use of “awk”? A) Aligning sequences with BLAST B) Extracting the 5th column from a tab-delimited annotation file C) Visualizing a phylogenetic tree D) Converting FASTQ to FASTA Answer: B Explanation: awk excels at column-based text processing, useful for parsing annotation files. Question 46. Which of the following statements about “percent identity” and “percent similarity” is correct? A) Percent identity counts only exact matches; percent similarity also includes conservative substitutions. B) Both metrics are identical. C) Percent similarity is always lower than percent identity. D) Percent identity includes gaps, while percent similarity does not. Answer: A
Question 50. When using the “cut” command to extract the first 10 characters of each line in a FASTA file, which option is appropriate? A) cut -c 1-10 file.fasta B) cut -f 1-10 file.fasta C) cut -d ‘>’ -f 1 file.fasta D) cut -s 10 file.fasta Answer: A Explanation: -c specifies character positions; 1-10 extracts the first ten characters. Question 51. Which of the following best describes a “gap extension penalty”? A) The cost added each time a gap is opened B) The cost added for each additional base in an existing gap C) The reward for extending a gap D) The penalty for mismatches only Answer: B Explanation: Gap extension penalties are applied per base after the initial gap opening. Question 52. In BLAST results, a high “bit score” indicates: A) A low-quality alignment B) A high-scoring, statistically significant alignment C) The length of the query sequence D) The number of gaps in the alignment Answer: B Explanation: Bit score normalizes raw scores; higher values reflect better alignments. Question 53. Which of the following is a typical use of the “sed” command in sequence file processing? A) Counting the number of sequences B) Replacing all “U” nucleotides with “T” in an RNA FASTA file
C) Performing a multiple sequence alignment D) Visualizing a phylogenetic tree Answer: B Explanation: sed performs stream editing, such as character substitution across a file. Question 54. The term “phylogeny” refers to: A) The physical structure of a protein B) The evolutionary history and relationships among organisms or genes C) The process of DNA replication D) The number of reads in a sequencing run Answer: B Explanation: Phylogeny studies evolutionary lineage and relatedness. Question 55. In a FASTQ file, the quality scores are encoded as ASCII characters. Which encoding is most commonly used for Illumina data? A) Phred+ B) Phred+ C) Sanger only D) None of the above Answer: A Explanation: Modern Illumina platforms use Phred+33 encoding for quality scores. Question 56. Which of the following statements about “local” vs. “global” alignment is FALSE? A) Global alignment aligns end-to-end of both sequences. B) Local alignment can detect shared motifs in otherwise unrelated sequences. C) Global alignment is always faster than local alignment. D) Local alignment may produce a shorter alignment region than the full length. Answer: C
Question 60. The “percent GC content” of a DNA sequence is calculated as: A) (G + C) / (A + T + G + C) × 100 B) (A + T) / total length × 100 C) (G – C) / total length × 100 D) (G + C) / total length × 100, where total length excludes ambiguous bases Answer: A Explanation: GC% = ((G + C) / total nucleotides) × 100. Question 61. Which of the following best explains why a high-scoring pair (HSP) is important in BLAST? A) It represents the longest possible alignment. B) It is the seed from which the full alignment is extended. C) It is the only alignment reported. D) It determines the GC content of the query. Answer: B Explanation: BLAST identifies HSPs as initial exact or near-exact matches, then extends them to form the final alignment. Question 62. In a basic script to batch-convert multiple FASTQ files to FASTA, which command would be central? A) seqtk seq -A file.fastq > file.fasta B) blastn -query file.fastq -out file.fasta C) grep “>” file.fastq > file.fasta D) awk ‘{print $1}’ file.fastq > file.fasta Answer: A Explanation: seqtk (or similar) with the “-A” flag converts FASTQ to FASTA format. Question 63. Which of the following is NOT a typical feature of a “low-complexity” region in a protein? A) Repetitive amino-acid composition B) Low information content
C) High sequence conservation across species D) Often masked before alignment Answer: C Explanation: Low-complexity regions are usually variable and may be masked; high conservation is not typical. Question 64. The “NCBI Entrez” system allows users to: A) Perform BLAST searches only B) Retrieve data across multiple NCBI databases via a unified interface C) Edit GenBank records directly D) Run phylogenetic analyses online Answer: B Explanation: Entrez integrates access to NCBI’s suite of databases (PubMed, GenBank, etc.). Question 65. Which of the following is a correct interpretation of an E-value of 1e-5 in a BLAST hit? A) One in 100,000 random alignments would achieve a similar score or better. B) The alignment covers 5 % of the query. C) The sequences are 95 % identical. D) The hit is guaranteed to be homologous. Answer: A Explanation: An E-value of 1e-5 indicates low probability of the match occurring by chance. Question 66. In a FASTA file, which character is used to denote the start of a comment line? A) ‘;’ B) ‘#’ C) ‘>’ D) ‘@’
