Q.22 The most widely used program for multiple sequence alignment is
- (A) BLAST
- (B) FASTA
- (C) CLUSTAL
- (D) Chime
The most widely used program for multiple sequence alignment is CLUSTAL, renowned for its progressive alignment algorithm and user-friendly interface. This SEO-optimized article answers the MCQ: The most widely used program for multiple sequence alignment is (A) BLAST, (B) FASTA, (C) CLUSTAL, (D) Chime—essential for bioinformatics, molecular biology, and biotechnology students working with sequence analysis.
Correct Answer: Option (C) CLUSTAL
CLUSTAL (originally ClustalW, now Clustal Omega) dominates multiple sequence alignment through progressive alignment: builds guide tree via distance matrix, aligns most similar sequences first, progressively adds distant sequences while maintaining gaps.
ClustalW citations exceed 100,000; Omega handles thousands of sequences rapidly. Features include adjustable gap penalties, hydrophobicity tables, and output formats (PHYLIP, NBRF) for phylogenetic analysis (Q.17) and isoschizomer pattern prediction (Q.14).
Explanation of All Options
Each tool serves distinct alignment purposes:
-
(A) BLAST: Incorrect. Database similarity search (local alignment), not multiple sequence alignment.
-
(B) FASTA: Incorrect. Faster sequence database search tool, primarily pairwise alignments.
-
(C) CLUSTAL: Correct. Gold standard for multiple sequence alignment of DNA/protein families.
-
(D) Chime: Incorrect. Molecular visualization plugin for RasMol/Chimera, not alignment software.
Option Primary Function Alignment Type Multiple Sequence? (A) BLAST Database search Local (BLASTP/N) No (B) FASTA Sequence similarity Pairwise/global Limited (C) CLUSTAL Multiple alignment Progressive Yes (D) Chime 3D visualization None No Biotechnology Applications
CLUSTAL alignments underpin primer design for hairy root transformation (Q.11), YAC insert verification (Q.4), LPS gene family analysis (Q.18), and phylogenetic tree construction (Q.17). Your molecular genetics workflow benefits from Clustal Omega’s scalability for microbial genomics and synthetic seed marker development.
-
