Multiple sequence alignment (MSA) is a bioinformatics technique used to align three or more biological sequences, which can be proteins, DNA, or RNA. The main goal of MSA is to identify similarities and differences among the sequences, enabling researchers to infer evolutionary relationships, functionally conserved regions, and structural features.
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A multiple sequence alignment places three or more sequences in corresponding columns, inserting gaps where needed. The arrangement represents a hypothesis about positional correspondence and can support phylogenetics or detection of conserved motifs. A column can be reliably aligned in one region and ambiguous in another. Adding sequences can clarify shared structure but also introduce difficult divergent regions, so the alignment itself requires evaluation before downstream inference. [ref]
Amino acid substitution matrices from protein blocks by Steven Henikoff and Jorja G. Henikoff. 1992, conserved protein blocks and aligned positions