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A sequence alignment is am arrangement of sequences of proteins, nucleotides, amino acids, DNA or RNA for the study about the similarity resulting from relationships that may be functional or structural between the sequences.  Such sequence alignment may be divided into two classifications, which are global alignments and local alignments.  Amongst these two, local alignments are more preferable, but the calculation becomes very difficult. 

A matrix contains the protein residues arranged in rows with gaps intervening in between the residues.  Consequently, the similar sequences appear in columns.  The quality of the scoring function determines the quality of the alignments.  For the reason of comparison, sometimes it is beneficial to carry out the same alignments with various choices. Sequence alignments are also used for sequences, which are not biological. These include sequences present in natural language and those in financial data.  

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