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Sequence Alignment: Pairwise and Multiple Alignment Methods

• Pairwise alignment is aligning two nucleic acid or two protein sequences to find the best match.
• Multiple alignment is aligning more than two sequences to identify regions of similarity for evolutionary relationship and construction of phylogenetic trees.
• Clustal Omega is one of the tools used for multiple sequence alignment.
• Dynamic programming is a method of solving complex problems by breaking them into simpler subproblems, which is used for both pairwise and multiple sequence alignment.
• Dot matrix or dot plot method is the basic sequence alignment method that uses dots to represent matches between two sequences.
• Global and local alignment final results are given as alignment score, and gaps are introduced to improve alignment.
• Gap penalty value is subtracted from the total alignment score to obtain the final alignment score.
• A gap-opening penalty value is assigned for each gap opened, and a gap-extension penalty value is assigned for each gap extended.
• Default values of -10 for gap-opening penalty and -1 for gap-extension penalty are commonly used.
• Raw alignment score is calculated using a formula that includes total score for identities, total score for mismatches, and total gap penalty.
• Heuristic methods (algorithms) like BLAST and FASTA are used for sequence alignment to estimate the best solution without considering every possible solution and save time.
• BLAST searches for homologous sequences with short, high-scoring similarity regions called words or hits, and FASTA searches for matching sequence patterns called k-tuples or ktup.