BMC Bioinformatics

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

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

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