115. Which one of the following CANNOT be used for progressive global multiple sequence
alignment?
A. ClustalW
B. LALIGN
C. PILEUP
D. T-COFFEE

Detailed Explanation:

Multiple sequence alignment (MSA) is a fundamental method used in bioinformatics to align three or more biological sequences (protein or nucleic acid) to identify regions of similarity.

Progressive global MSA is a widely used approach that builds the final alignment step-by-step:

1. Start with the most similar pair.

2. Progressively align the rest based on a guide tree.

Let’s look at the listed tools:

A. ClustalW

• Supports progressive alignment.

• One of the most popular global MSA tools.

• Builds a guide tree and aligns sequences in a progressive manner.

B. LALIGN

• Does NOT support progressive global MSA.

• Instead, it performs local pairwise sequence alignments.

• It is a variant of the Smith-Waterman algorithm, optimized for detecting local similarities between two sequences.

C. PILEUP

• Supports progressive alignment.

• An older tool but uses hierarchical clustering to align sequences progressively.

D. T-COFFEE

• Supports progressive alignment.

• Enhances accuracy by combining information from pairwise alignments and integrating it into a consensus.

Final Answer:

B. LALIGN

LALIGN is specialized for local alignment, not progressive global multiple sequence alignment, and is therefore the correct choice that does not fit in this category.