Figure 1.

Schematic diagram of each step of our heuristic method. (a) The process of enumerating the subsequences from the candidate-genes. The green sequence represents a candidate-gene, and the blue sequences represent the subsequences that were derived from this candidate-gene by the sliding scan. (b) Diagram of the relationship between the subsequences. The blue lines C₁, C₂,…, C₈ represent the candidate-genes, and S₁, S₂,…, S₁₁ are the subsequences that were enumerated from these candidate-genes. A solid line between two subsequences indicates that the two subsequences are neighbors, and the dotted line indicates that the two subsequences are far_neighbors. Each subsequence is marked as a candidate for a qualified sequence. (c) Diagram of the relationship between the marked subsequences after the far_neighbor examination. The subsequences S₅, S₉ and S₁₀ are unmarked because they all contained a far_neighbor. However, S₂ is still marked because one of its neighbors was located in C₄, and its far_neighborS₅ was also located in C₄. In this situation, we are not concerned about whether the siRNA that was designed based on S₂ will recognize S₅ because C₄ is already the target gene of this siRNA. Therefore, S₂ is still marked as a candidate for the qualified sequence. (d) Diagram of the relationship between the marked subsequences after the powerful subsequence examination. S₁, S₄ and S₆ are unmarked because they are not powerful subsequences and are all dominated by S₂. (e) Diagram of the relationship between the marked subsequences after the excluded-gene hit examination. E_i is one of the excluded-genes, and the dot-dashed line indicates that the Hamming distance between a marked subsequence and a substring that is located in an excluded-gene is less than d_N; this scenario also indicates that this marked subsequence contains an excluded-gene hit. Because any subsequences that contain an excluded-gene hit will be unmarked, S₁₁ is unmarked.