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Fig. 3 | Algorithms for Molecular Biology

Fig. 3

From: Coordinate systems for supergenomes

Fig. 3

Comparison of different graph definitions. Consider an alignment comprising of five MSA blocks (\(B_1\), \(B_2\), \(B_3\), \(B_4\), \(B_5\)) in four assemblies (indicated by different edge colors: \(\mathcal {G}_1\) blue, \(\mathcal {G}_2\) green, \(\mathcal {G}_3\) orange, \(\mathcal {G}_4\) purple), consisting of a total of sequence intervals denoted by \(\beta _{k,l}=(\mathcal {G}_l,c_{k,l},i_{k,l},j_{k,l},+1) \in B_k\) and \(\bar{\beta }_{k,l}=(\mathcal {G}_l,c_{k,l},i_{k,l},j_{k,l},-1) \in B_k\) for positive and negative orientation, respectively. In the drawings, block \(B_i\) is simply denoted by i. Most of the edges in the different graphs represent the adjacency of two intervals in one of the constituent assemblies. These edges are displayed in the corresponding color. (i) Genome order and orientation of the intervals. Every line shows one assembly and the order on this assembly. (ii) The supergenome graph. (iii) The bidirected graph. Note that the edges are the same as in the supergenome graph except for the shown direction. (iv) The sequence graph of Haussler et al. [29]. Note that the edges (3,4) and (5,2) are not part of the graph because of the change in orientation. (v) The enredo graph. An example of the other special graph structures discussed in Kehr et al. [58]

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