Question

Clustal W is a multiple alignment program available either as a stand-alone or on-line program.

• A. exhaustive
• B. block based
• C. progressive
• D. iterative

Hint:

• Clustal W / Clustal Omega Popular programs for multiple sequence alignment.
• Employ a progressive alignment} strategy: 1. Calculate all pairwise alignments and similarities. 2. Construct a guide tree based on similarities. 3. Align sequences progressively following the guide tree ("once a gap, always a gap" for simple progressive).
• This is a heuristic approach, not guaranteed to find the optimal MSA.
• More advanced MSA tools may use iterative refinement or other algorithms.

Answer 1

The Correct Option is C

Clustal W is a widely used multiple alignment program in biotechnology. The correct answer to the given question regarding the type of algorithm employed by Clustal W is progressive.

Here's a brief explanation:

Clustal W utilizes a progressive alignment strategy, which means the program first conducts a pairwise alignment to construct a guide tree, and then it progressively aligns sequences by following the order in the guide tree. This method allows Clustal W to efficiently handle multiple sequence alignments, making it a popular choice for researchers in the field.

The option choices were:

Option	Description
exhaustive	This involves examining all possible solutions, which is not used by Clustal W due to computational complexity.
block based	This emphasizes short, highly conserved regions (blocks) but is not how Clustal W functions.
progressive	Correct. This is the method used by Clustal W for aligning sequences.
iterative	Refers to repeatedly refining the alignment, not primarily the method used by Clustal W.

Therefore, the correct answer is: progressive.