Figure 2From: Designing multiple degenerate primers via consecutive pairwise alignmentsPerformance of PT-MIPS [2] for different input parameters. (left) beam size = 10, variable pairwise fragment size; (right) pairwise fragment size = 6, variable beam size. A set of 40 random sequences each of length50 is used to generate primers each of length 15 and maximum degeneracy of 104. Increasing the beam size or decreasing the pairwise fragment size improves the algorithm performance slightly, but increases the computation time significantly, making large analyses like that of Figure 3 impossible.Back to article page