Fig. 3
From: REHUNT: a reliable and open source package for restriction enzyme hunting
Good-suffix shift 1 rule. N is the length of the input sequence and M is the length of the enzyme recognition sequence. Sequence (n) and Enzyme (m) represent the nucleotide at the n-th position in the input sequence and the nucleotide at the m-th position in the enzyme recognition sequence, respectively. Enzyme (m s , m e ) represents nucleotides from the m s -th position to the m e -th position in the enzyme recognition sequence. a Enzyme recognition sequence is aligned from right to left: Enzyme (11) = Sequence (11), Enzyme (10) = Sequence (10), but Enzyme (9) ≠ Sequence (9). b Enzyme (5,6) is the suffix string of the Enzyme found, and Enzyme (4) ≠ Enzyme (9). The Enzyme window is then moved and Enzyme (4) is aligned to Sequence (9)