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Table 2 Precision and recall of our matching algorithm (aodp) and USEARCH using the 4Mycotoxins training set and the 4MicotoxinsBootstrap testing set

From: Cluster oligonucleotide signatures for rapid identification by sequencing

aodp
λ 8 16 24 32 40 8 16 24 32 40
ε Precision Recall
0.05 0.74 0.90 0.91 0.92 0.93 0.71 0.49 0.25 0.15 0.08
0.04 0.78 0.92 0.92 0.92 0.93 0.76 0.64 0.38 0.23 0.14
0.03 0.83 0.95 0.95 0.95 0.96 0.80 0.78 0.55 0.38 0.24
0.02 0.89 0.97 0.97 0.97 0.97 0.84 0.88 0.74 0.57 0.43
0.01 0.95 0.99 0.99 0.99 0.99 0.87 0.91 0.88 0.78 0.68
0.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
USEARCH
χ 4 16 64 256 1024 4 16 64 256 1024
ε Precision Recall
0.05 0.21 0.40 0.62 0.88 0.98 0.19 0.38 0.60 0.84 0.94
0.04 0.21 0.41 0.63 0.89 0.98 0.20 0.38 0.59 0.83 0.92
0.03 0.21 0.41 0.64 0.89 0.99 0.20 0.39 0.60 0.84 0.93
0.02 0.22 0.43 0.66 0.91 0.99 0.20 0.40 0.61 0.84 0.92
0.01 0.24 0.45 0.67 0.92 1.00 0.21 0.41 0.61 0.83 0.90
0.00 0.28 0.50 0.72 0.95 1.00 0.26 0.50 0.72 0.95 1.00
  1. Rows have a given error rate ε For aodp, columns have a given signature length λ. For USEARCH, columns have a given value χ for the “maxaccepts” parameter. Cells where USEARCH outperforms aodp on the F measure are in bold. Cells where aodp outperforms USEARCH on the F measure for χ≤256 are also in bold