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Figure 10 | BMC Bioinformatics

Figure 10

From: Designing multiple degenerate primers via consecutive pairwise alignments

Figure 10

Searching different combinations of sequences to obtain the optimum one. PAMPS starts with the first sequence as P1 (top node) and either merges the second sequence with it (left branch) or adds the second sequence as P2 (right branch). The numbers in the nodes represent the number of primers in the corresponding primer sets. Each node is expanded from its left branch first, continuing with the right branches in order. To avoid exponential growth of the tree, some nodes are not expanded. For example, node B has the same number of primers as A and covers the same number of sequences. Hence, it is expanded only if the sum of scores of its primers exceeds that of A. Similarly, C is only expanded if it outscores both A and B.

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