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Figure 2 | Algorithms for Molecular Biology

Figure 2

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

Figure 2

Intuition of Triplet algorithm. (A) Intuition of Triplet algorithm. A triplet consists of 12 mers l 1, l 2 and l 3. l 1 and l 2, l 1 and l 3, and l 2 and l 3 contain 4, 6 and 5 differences respectively as labeled in the lines connecting them. Use the 12 mer as the center to draw an imaginary circle. Each circle denotes the set of neighboring 12 mers that are no more than 3 differences from the center 12 mer. In other words, each circle represents the set of putative motifs that generate the center 12 mer. Note that we do not actually generate the set of putative motifs. Centroid l mer is denoted by a diamond shape dot. The goal of the algorithm is to uncover all members of the set in the intersection (dark gray) of the three sets. (B) Centroid l mer construction. Shown are three patterns of columns viz. same nucleotide in three 12 mers Pi (solid line vertical boxes in positions 1, 5, 6, 8 and 10), all different nucleotides across three 12 mers Pnc (vertical box with dashed boundary in position 11), and two out of three 12 mers having the same nucleotides Pmn (dotted line vertical boxes in positions 2, 3, 4, 7, 9, and 12). The centroid l mer is constructed in stage 1 of Triplet algorithm described in the text. The number of identical positions between the centroid l mer and l 1, l 2 and l 3, is represented by the score vector and the selection of nucleotides encoded in move vector (C) Structure of move vector. (D) Exploratory scheme discovery from stage 2 of Triplet algorithm. Centroid l mer constructed in Figure 2B is modified by the composite operation of sac(P12) and nc(3,1) to create three extra motifs near its neighborhood. (E) Example of applying rule 13 to create a new move vector in (D).

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