BMC Bioinformatics

Table 2 Benchmark results of the thirteen prediction tools. Equations 1-4 are used to measure the predictive performance of these tools. (Abbreviations used: Sn = Sensitivity; Spc = Specificity; Acc = Accuracy; MCC = Matthews' Correlation Coefficient). ¹ Used with HMMER 2.3.2 with cut-off score set at -5 [26] and the updated model [20]; ² Version 3.0; ³ Authors updated system with UniProt 14.6 (Swiss-Prot Release 57.0) [3, 62]; ⁴ Version 1.0.1.

From: A comprehensive assessment of N-terminal signal peptides prediction methods

	Experiment 1				Experiment 2				Experiment 3
Methods	Sn	Spc	Acc	MCC	Sn	Spc	Acc	MCC	Sn	Spc	Acc	MCC
Philius	0.704	0.952	0.828	0.677	0.742	0.968	0.855	0.729	0.728	0.961	0.844	0.708
Phobius	0.637	0.978	0.807	0.654	0.749	0.982	0.865	0.752	0.711	0.987	0.849	0.726
PrediSi	0.726	0.974	0.850	0.723	0.768	0.986	0.877	0.773	0.750	0.974	0.862	0.742
RPSP	0.730	0.989	0.859	0.744	0.805	0.996	0.901	0.816	0.794	1.000	0.897	0.811
SigCleave	0.541	0.878	0.709	0.445	0.613	0.823	0.718	0.446	0.618	0.860	0.739	0.493
SigHMM¹	0.707	0.937	0.822	0.662	0.561	0.963	0.762	0.572	0.596	0.952	0.774	0.587
SignalP² ANN	0.785	0.959	0.872	0.756	0.856	0.965	0.910	0.826	0.842	0.987	0.914	0.838
SignalP² HMM	0.759	0.952	0.856	0.725	0.832	0.974	0.903	0.814	0.833	0.969	0.901	0.810
Signal-BLAST³	0.978	0.815	0.896	0.803	0.881	0.809	0.845	0.692	0.825	0.794	0.809	0.619
Signal-CF	0.648	0.900	0.774	0.566	0.768	0.905	0.836	0.679	0.750	0.890	0.820	0.647
Signal-3L	0.737	0.889	0.813	0.633	0.786	0.920	0.853	0.712	0.715	0.934	0.825	0.665
SOSUIsignal	0.189	0.926	0.557	0.170	0.232	0.925	0.578	0.217	0.232	0.921	0.577	0.212
SPOCTOCUS⁴	0.393	0.907	0.650	0.350	0.502	0.902	0.702	0.441	0.408	0.899	0.654	0.352

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