Table 2. Comparison of PANNZER2, using the ARGOT scoring function, ARGOT2 and eggNOG-mapper. Tests were repeated by a) omitting annotations with IEA, ISS and ND evidence codes and b) using all GO annotations. Evaluation was repeated using 5000 query subsets of the test data to allow for comparison with ARGOT2. We show results with Fmax and with Smin. Note that higher values of Fmax and lower values of Smin show better performance. PANNZER2 outperforms both eggNOG-mapper and ARGOT2 methods consistently.

		Comparisons with the whole dataset				Comparisons with subsets of the data
Truth Set = >		No IEA, ISS, ND		All evidence codes		No IEA, ISS, ND			All evidence codes
Ontology	Metric	PANZ2	eggNOG	PANZ2	eggNOG	PANZ2	eggNOG	ARGOT2	PANZ2	eggNOG	ARGOT2
BP	Fmax	0.699	0.615	0.786	0.640	0.700	0.613	0.608	0.784	0.629	0.682
MF	Fmax	0.708	0.640	0.867	0.591	0.708	0.641	0.649	0.858	0.591	0.777
CC	Fmax	0.823	0.752	0.863	0.774	0.820	0.749	0.757	0.853	0.773	0.776
BP	Smin	31.401	45.918	27.643	45.376	30.264	45.920	38.375	27.474	46.408	42.483
MF	Smin	9.597	12.942	6.701	15.995	9.682	12.890	11.609	7.196	16.06	11.946
CC	Smin	9.415	14.053	7.917	14.114	9.645	14.184	13.418	8.692	14.401	15.587