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. |