Question

Clustal W is a \rule{1cm{0.15mm} 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 (and its successor Clustal Omega) is a widely used computer program for performing multiple sequence alignment (MSA). Multiple sequence alignment aligns three or more biological sequences (DNA, RNA, or protein). Clustal W employs a progressive alignment heuristic method. The main steps are: 1. Pairwise Alignments: All pairs of sequences are aligned (e.g., using a global alignment algorithm like Needleman-Wunsch) to calculate pairwise similarity scores. 2. Guide Tree Construction: A guide tree (phylogenetic tree or dendrogram) is constructed based on the pairwise similarity scores. This tree represents the presumed evolutionary relationships between the sequences, with more similar sequences clustering together. 3. Progressive Alignment: The sequences are then progressively aligned according to the branching order of the guide tree. Starting with the most closely related pairs, alignments are performed, and then these alignments (or consensus sequences/profiles derived from them) are aligned with other sequences or alignments, moving up the guide tree until all sequences are incorporated into the final multiple alignment. This progressive approach is a heuristic, meaning it does not guarantee finding the mathematically optimal multiple alignment (which is computationally very expensive for many sequences), but it generally produces good quality alignments in a reasonable amount of time. Let's analyze the options: (a) exhaustive: Exhaustive methods (like dynamic programming for MSA) are computationally too intensive for more than a few sequences. Clustal W is heuristic. (b) block based: While MSA can identify conserved blocks, Clustal W's overall strategy is progressive, not primarily "block based" in the sense of programs like DIALIGN or Block Maker. (c) progressive: This accurately describes the core algorithmic strategy of Clustal W. (d) iterative: While some MSA programs use iterative refinement (e.g., MUSCLE, MAFFT, and Clustal Omega does incorporate iterative steps), the fundamental approach of Clustal W (the original) is primarily progressive based on a fixed guide tree. Iterative methods refine an initial alignment through multiple cycles. Therefore, Clustal W is a progressive multiple alignment program. \[ \boxed{\text{progressive}} \]