Skip to main content
Figure 1 | BMC Genomics

Figure 1

From: An efficient RNA interference screening strategy for gene functional analysis

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 C 1 , C 2 ,…, C 8 represent the candidate-genes, and S 1 , S 2 ,…, S 11 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 S 5 , S 9 and S 10 are unmarked because they all contained a far_neighbor. However, S 2 is still marked because one of its neighbors was located in C 4 , and its far_neighbor S 5 was also located in C 4 . In this situation, we are not concerned about whether the siRNA that was designed based on S 2 will recognize S 5 because C4 is already the target gene of this siRNA. Therefore, S 2 is still marked as a candidate for the qualified sequence. (d) Diagram of the relationship between the marked subsequences after the powerful subsequence examination. S 1 , S 4 and S 6 are unmarked because they are not powerful subsequences and are all dominated by S 2 . (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, S 11 is unmarked.

Back to article page