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Table 1 Five basic operations for triplet processing of iTriplet algorithm

From: iTriplet, a rule-based nucleic acid sequence motif finder

Operations Description Examples based on Figure 2D if possible
sac(Pmn) Instead of choosing the dominant nucleotide from Pmn column, choose the odd nucleotide. sac(P12), take 'G' at position 3 from l 3 instead of 'C' from l 1 or l 2
compl(Pmn) Instead of choosing the dominant or odd nucleotide from Pmn column, choose nucleotides complementary to them. Apply on the 2nd column, compl(P23), take nucleotides complementary to 'G' and 'T', i.e. choose 'A' or 'C' for position 2.
nc(i, j) Instead of taking nucleotide from l meri, choose from l merj in a Pnc column. Apply nc(3,1) to position 11. Instead of choose 'A' from l 3, choose 'T' from l 1 at position 11.
nc(i,0) Instead of taking nucleotide from l meri, choose from the complementary nucleotide of a Pnc column. Apply nc(3,0) to position 11. Instead of choose 'A' from l 3, assign the complementary nucleotide 'G' to position 11.
sac_i(Pi) Instead of keeping the nucleotide identical to all lmers in the triplet, take the three complementary nucleotides. Apply sac_i(Pi) to position 1. Take 'A', 'G' or 'T' instead of 'C' at position 1.