Question 1

What is the primary purpose of Multiple Sequence Alignment (MSA)?

Accepted Answer

To compare three or more biological sequences simultaneously

Answer

To identify protein structures

Answer

To perform genome assembly

Answer

To sequence DNA molecules

Question 2

Which of the following is a commonly used MSA tool?

Accepted Answer

Clustal Omega

Answer

PyMOL

Answer

BLAST

Answer

Primer3

Question 3

What does a gap in a sequence alignment represent?

Accepted Answer

Insertion or deletion event (indel)

Answer

Sequencing error

Answer

Protein domain

Answer

Mutation hotspot

Question 4

Which alignment strategy is used by Clustal Omega?

Accepted Answer

Progressive alignment

Answer

Dot matrix alignment

Answer

Local alignment

Answer

Random alignment

Question 5

MSA is most useful for identifying:

Accepted Answer

Conserved regions among sequences

Answer

Cell morphology

Answer

Chromosome numbers

Answer

Protein purification methods

Question 6

Which algorithm is commonly used in MUSCLE?

Accepted Answer

Iterative refinement

Answer

Restriction mapping

Answer

Needleman-Wunsch only

Answer

Sanger sequencing

Question 7

What is a guide tree in MSA?

Accepted Answer

A phylogenetic-like tree used to determine alignment order

Answer

A protein structure model

Answer

A database of sequences

Answer

A tree showing species distribution

Question 8

Which scoring matrix is frequently used for protein sequence alignment?

Accepted Answer

BLOSUM62

Answer

PAM0

Answer

FASTA Matrix

Answer

GC Content Matrix

Question 9

Which MSA tool is known for high accuracy but relatively slower performance?

Accepted Answer

T-Coffee

Answer

Primer-BLAST

Answer

MAFFT

Answer

BLAT

Question 10

Multiple sequence alignments are commonly used for:

Accepted Answer

Phylogenetic analysis

Answer

Cell culture maintenance

Answer

Protein purification

Answer

Microscopy imaging

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