Figure 1.

Overview of the prediction method for SMB gene clusters. (a) Broken lines represent homologous gene pairs between two genomes. Each pair of ‘x_i1’–‘y_j1’, ‘x_i2’–‘y_j2’, ‘x_i4’–‘y_j4’, ‘x_i5’–‘y_j8’, ‘x_i6’–‘y_j5’ and ‘x_i8’–‘x_j7’ represents a homolog. The x_i and y_j represent genes in the first and the second genomes, respectively. (b) The genes were aligned in the genome using the Smith–Waterman algorithm (Param2 = −1). Pairs of contiguous genes from ‘x_i1’ to ‘x_i8’ in genome 1 and from ‘y_j1’ to ‘y_j7’ represent an example identified as a seed for predicting a gene cluster (R₀ or other seed regions). (c) The seed was extended until the prescribed length (Param3 = 35). The symbols l_x and l_y represent the numbers of genes added to the seed region of the first and the second genomes, respectively. X and Y represent extended clusters in the first and the second genomes, respectively. (d) The boundaries were corrected (Param4 = −1), and a pair of candidate gene clusters, ‘x_i1’ through ‘x_i8’ and ‘y_j1’ through ‘y_j8’, was identified. The symbols i_begin and i_end represent the locations of the genes at the beginning and end, respectively, of the cluster in the first genome. The symbols j_begin and j_end represent the corresponding gene locations in the second genome. The CB value is the sum of the maximum scores for the upstream and the downstream boundaries of a predicted cluster. The integers are indicated as an example for the particular alignment of clusters represented in this figure. (e) Synteny analysis was performed to distinguish the SMB gene cluster from the syntenic block (SB). The SB, a subset of X and Y, represents a set of genes aligned to create a contiguous block of orthologous gene pairs located within the defined distance between neighboring genes (Param5 = 10 kb). The above parameters are examples and not necessarily those used for the actual analyses.