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3.1 Pairwise Alignment & Algorithms — Test 1
Q1. A sequence alignment is performed mainly to:✓ Identify regions of similarity that may indicate relationship or function
Q2. A global alignment, as produced by the Needleman-Wunsch algorithm, aligns:✓ The entire length of both sequences
Q3. A local alignment, as produced by the Smith-Waterman algorithm, finds:✓ The best-matching local region(s) between sequences
Q4. Both Needleman-Wunsch and Smith-Waterman are based on the technique of:✓ Dynamic programming
Q5. A dot-plot (dot-matrix) analysis compares two sequences by:✓ Placing a dot where residues match, revealing diagonals of similarity
Q6. In an alignment, a 'gap' represents:✓ An insertion or deletion (indel) in one sequence relative to the other
Q7. In comparing alignment quality, 'identity' refers to:✓ The percentage of positions with exactly the same residue
Q8. A pairwise alignment, by definition, aligns:✓ Exactly two sequences
Q9. A global alignment is most appropriate when the two sequences are:✓ Of similar length and expected to be related over their whole length
Q10. Local alignment is especially useful for:✓ Finding conserved domains shared by otherwise different sequences
Q11. In a dot-plot, a long unbroken diagonal line indicates:✓ A region of strong similarity between the two sequences
Q12. The score of an alignment is calculated using:✓ A scoring matrix for matches/mismatches plus gap penalties
Q13. The main advantage of dynamic-programming alignment over simple heuristics is that it:✓ Guarantees the optimal alignment for the chosen scoring scheme
Q14. Alignment of two sequences can provide evidence of:✓ Homology (common evolutionary origin)
Q15. Conservative substitutions in an alignment are those where:✓ One residue is replaced by a chemically similar one
Q16. When aligning two sequences, increasing the gap penalty tends to produce alignments with:✓ Fewer gaps
Q17. Repeated elements within a sequence often appear in a dot-plot as:✓ Multiple parallel diagonal lines
Q18. The key difference between identity and similarity in alignments is that similarity also counts:✓ Chemically similar (conservative) substitutions
Q19. Affine gap penalties distinguish between:✓ Opening a gap and extending an existing gap
Q20. Match each alignment concept with its description and select the correct option.✓ A-ii, B-iv, C-iii, D-i