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Table 3 Sensitivity comparison of computed spaced seeds for PatternHunter

From: Efficient computation of spaced seeds

w

N

p

BLAST

PH

PHII

Mandala

Iedera

SpEED

Fast HC

   

(contig.)

(spaced)

(16 seeds)

    

11

64

0.70

30.0196

46.7122

92.4114

92.3811

92.0708

93.2526

93.3406

11

64

0.75

49.4494

69.5844

98.4289

98.4320

98.3391

98.6882

98.7156

11

64

0.80

71.3993

88.2070

99.8449

99.8448

99.8366

99.8820

99.8859

  1. Sensitivity comparison with Mandala, Iedera, and SpEED (results from [18]). Seeds were computed with the same parameters as those of PatternHunter II. Fast HC (sensitivity values in bold) is the best in all cases. The sensitivity of the original seeds is significantly improved.
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BMC Research Notes

ISSN: 1756-0500

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