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Table 5 Sensitivity comparison of computed spaced seeds of MegaBLAST weight

From: Efficient computation of spaced seeds

w

N

p

MegaBLAST

1 seed

Fast HC

   
   

(contig.)

(spaced)

2 seeds

4 seeds

8 seeds

16 seeds

28

100

0.90

39.1436

69.3241

79.6629

87.5674

92.7762

95.9170

28

150

0.90

55.4870

87.6426

93.4308

97.0118

98.7430

99.5137

28

200

0.90

67.4412

94.9876

97.8936

99.2937

99.7877

99.9409

  1. Using Fast HC, we computed multiple seeds with the same weight as the default seed of MegaBLAST for similarity 90% and N ∈ {100, 150, 200}. The sensitivities of the new seeds are much higher than those of MegaBLAST. The values in bold show that the new 16, 2 and 2 seeds, respectively, reach sensitivities over 95% for N equal to 100, 150, and 200, respectively.