Quick revision: every question with its correct answer. For the full explanation, open the test and tap View Solution.
3.4 Multiple Sequence Alignment — Test 1
Q1. A multiple sequence alignment (MSA) involves aligning:✓ Three or more sequences simultaneously
Q2. ClustalW performs multiple sequence alignment using a strategy called:✓ Progressive alignment
Q3. In progressive alignment, the order in which sequences are added is determined by a:✓ Guide tree (based on pairwise similarities)
Q4. A major use of a multiple sequence alignment is to:✓ Reveal conserved regions/motifs across a set of sequences
Q5. Besides ClustalW/Clustal Omega, other widely used MSA programs include:✓ MUSCLE and T-Coffee
Q6. A consensus sequence derived from an MSA shows, at each position, the:✓ Most common residue among the aligned sequences
Q7. Compared with pairwise alignment, multiple sequence alignment is:✓ Computationally more complex
Q8. A profile or hidden Markov model (HMM) can be built from an MSA to:✓ Capture position-specific conservation for sensitive searching
Q9. In ClustalW alignment output, an asterisk (*) beneath a column indicates:✓ A fully conserved position (identical in all sequences)
Q10. The 'sum-of-pairs' score is one way to evaluate an MSA by:✓ Summing the scores of all pairwise comparisons within each column
Q11. Iterative refinement methods improve an MSA by:✓ Repeatedly realigning subsets to correct early mistakes
Q12. MSAs are essential inputs for:✓ Phylogenetic tree construction
Q13. Gaps in a multiple sequence alignment represent:✓ Insertions or deletions relative to other sequences
Q14. Conserved columns in an MSA are biologically important because they often indicate:✓ Functionally or structurally critical residues
Q15. Clustal Omega is notable for being able to align:✓ Very large numbers of sequences efficiently
Q16. The guide tree used in progressive alignment is:✓ A rough tree used only to order alignment, not a final phylogeny
Q17. A practical risk of progressive alignment is that:✓ Errors made early (in aligning close sequences) propagate to the whole alignment
Q18. The output alignment file from ClustalW commonly has the extension:✓ .aln
Q19. A profile-based search (using an MSA-derived profile) is more sensitive than a single-sequence search because it:✓ Uses information from many related sequences at once
Q20. Match each MSA concept with its description and select the correct option.✓ A-iii, B-iv, C-i, D-ii