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Identity scoring

This is the simplest scoring scheme; amino acid pairs are classified into two types: identical and non-identical. Non-identical pairs are scored 0 and identical pairs given a positive score (usually 1). The scoring scheme is generally considered less effective than schemes that weight non-identical pairs, particularly for the detection of weak similarities [3][2]. The normalised sum of identity scores for an alignment is popularly quoted as ``percentage identity'', but this value can be useful to indicate the overall similarity between two sequences, there are pitfalls associated with the measure. These are discussed in section 4.1.1.