Question:medium
Which of the following methods is/are used for local alignment of nucleotide sequences?
Which of the following methods is/are used for local alignment of nucleotide sequences?
Show Hint
Smith-Waterman and BLAST are used for local alignment, whereas Needleman-Wunsch is used for global alignment and Neighbour-joining is used for phylogenetic analysis.
Updated On: Jun 5, 2026
- Smith-Waterman algorithm
- Needleman-Wunsch algorithm
- BLAST
- Neighbour-joining method
Show Solution
The Correct Option is A, C
Solution and Explanation
Step 1: Local vs global alignment.
Local alignment hunts for the best matching patch inside two sequences, while global alignment lines up the full length end to end.
Step 2: Check Smith-Waterman.
The Smith-Waterman method uses dynamic programming made specifically for local alignment, so A is true.
Step 3: Check Needleman-Wunsch.
Needleman-Wunsch is the global alignment method, so it does not fit local alignment and B is false.
Step 4: Check BLAST and neighbour-joining.
BLAST is a fast local alignment search against databases, so C is true. Neighbour-joining only builds phylogenetic trees, not alignments, so D is false.
Step 5: Answer.
\[ \boxed{A,\ C} \]
Local alignment hunts for the best matching patch inside two sequences, while global alignment lines up the full length end to end.
Step 2: Check Smith-Waterman.
The Smith-Waterman method uses dynamic programming made specifically for local alignment, so A is true.
Step 3: Check Needleman-Wunsch.
Needleman-Wunsch is the global alignment method, so it does not fit local alignment and B is false.
Step 4: Check BLAST and neighbour-joining.
BLAST is a fast local alignment search against databases, so C is true. Neighbour-joining only builds phylogenetic trees, not alignments, so D is false.
Step 5: Answer.
\[ \boxed{A,\ C} \]
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