Sequence alignment

Sequence alignment

Sequence alignment is a bioinformatics technique used to compare nucleotide or amino acid sequences to identify similarities or homologies between them. This process is crucial for understanding the structure, function, and evolutionary history of biological sequences.

A sequence alignment, produced by ClustalO, of mammalian histone proteins.

There are two main types of sequence alignment: pairwise alignment and multiple sequence alignment. Pairwise alignment compares two sequences, while multiple sequence alignment compares three or more sequences.

In pairwise alignment, algorithms such as Needleman-Wunsch and Smith-Waterman are commonly used. Needleman-Wunsch is a dynamic programming algorithm that finds the optimal alignment between two sequences by maximizing the number of matched characters and minimizing the number of gaps and mismatches. Smith-Waterman is similar but allows for local alignments, which are useful for finding similar regions within longer sequences.

Multiple sequence alignment is more complex due to the increased number of sequences involved. Algorithms like ClustalW and MUSCLE are frequently used for multiple sequence alignment. These algorithms aim to align sequences based on their shared evolutionary history, considering both sequence similarity and the conservation of functional and structural motifs.

Depicts the steps the ClustalW software algorithm uses for global alignments

Sequence alignment is crucial in various biological studies. In evolutionary biology, sequence alignment is used to construct phylogenetic trees, which depict the evolutionary relationships between organisms. In molecular biology, sequence alignment helps predict protein structure and function by identifying conserved amino acid residues. In medical research, sequence alignment is used to compare genetic sequences from different individuals to understand disease susceptibility and drug response.

--> Sequence alignment is a foundational technique in bioinformatics that plays a crucial role in understanding the complexities of biological sequences and their functions.


For more information , here is a explainer video: