A sequence alignment in bioinformatics is a way of arranging DNA, RNA, or protein primary sequences to emphasize their regions of similarity, which may indicate functional or evolutionary relationships between the genes or proteins in the query. Aligned sequences are typically written with their characters (generally representing amino acids or nucleotides) in columns into which gaps are inserted so that residues with identical or similar characters are aligned in the successive columns. If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In protein sequence alignment, the degree of similarity between amino acids occupying a particular position in the sequence can be interpreted as a rough measure of how conserved a particular region or sequence motif is among lineages. (more...)
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