Question

Which of the alignment does not assume that the two sequences in question have similarity over the entire length?

• A. Local
• B. Global
• C. Heuristic
• D. Clustal

Hint:

• Global Alignment (e.g., Needleman-Wunsch) Aligns sequences from end to end. Assumes overall similarity.
• Local Alignment (e.g., Smith-Waterman, BLAST, FASTA) Finds best matching segments/regions within sequences. Does not assume overall similarity. Useful for finding conserved domains or motifs.

Answer 1

The Correct Option is A

Sequence alignment is a way of arranging DNA, RNA, or protein sequences to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships. There are two main types of pairwise sequence alignment: 1. Global Alignment:

• Assumes that the two sequences are generally similar over their entire length.
• Attempts to align every residue in one sequence with a residue or a gap in the other sequence.
• Useful for comparing closely related sequences of similar length.
• Example algorithm: Needleman-Wunsch algorithm.

2. Local Alignment:

• Does not assume that the two sequences are similar over their entire length.
• Instead, it finds the regions of highest similarity between subsequences of the two sequences. It looks for conserved domains or motifs.
• Useful for comparing more distantly related sequences, sequences of different lengths, or finding conserved domains within larger sequences.
• Example algorithm: Smith-Waterman algorithm. BLAST is a heuristic method that performs local alignments.

Let's analyze the options: (a) Local alignment: This type specifically does not assume similarity over the entire length and seeks out the best matching sub-regions. This is the correct answer. (b) Global alignment: Assumes similarity over the entire length. (c) Heuristic: This refers to an approach or algorithm that finds an approximate solution, often faster than optimal algorithms (e.g., BLAST and FASTA are heuristic local alignment tools). It's a method type, not an alignment type (local vs. global) itself, though heuristic methods are often used for local alignments. (d) Clustal (e.g., ClustalW, Clustal Omega): This is a program for performing multiple sequence alignment (aligning three or more sequences), not pairwise alignment. Multiple sequence alignment often aims for a global-like alignment of the set of sequences. Therefore, local alignment does not assume similarity over the entire length. \[ \boxed{\text{Local}} \]