Table 2.

Performance comparison among different predictors on full test sets TS1 (63 RNAs), TS2 (30 RNAs), TS3 (54 RNAs), RNA-Puzzles (12 RNAs), TS80 (10 RNAs) and TS-rfam (69 RNAs) and reduced test sets TS1 (21 RNAs), TS2 (9 RNAs), TS3 (52 RNAs), RNA-Puzzles (7 RNAs), TS80 (10 RNAs) and TS-rfam (20 RNAs) after removing the sequences overlapping with RNAContact training data

	TS1			TS2			TS3			RNA-Puzzles			TS80			TS-rfam
	F1	Precision	Sensitivity	F1	Precision	Sensitivity	F1	Precision	Sensitivity	F1	Precision	Sensitivity	F1	Precision	Sensitivity	F1	Precision	Sensitivity
Full test sets
GREMLIN	0.242	0.228	0.258	0.146	0.156	0.136	0.065	0.463	0.035	0.118	0.258	0.077	0.259	0.207	0.345	0.123	0.182	0.093
plmDCA	0.338	0.342	0.334	0.269	0.261	0.279	0.233	0.387	0.166	0.194	0.367	0.131	0.333	0.393	0.289	0.256	0.284	0.233
mfDCA	0.348	0.301	0.414	0.307	0.244	0.412	0.343	0.313	0.379	0.271	0.254	0.291	0.353	0.372	0.335	0.301	0.247	0.387
PLMC	0.375	0.478	0.308	0.295	0.348	0.256	0.169	0.560	0.099	0.181	0.555	0.108	0.395	0.538	0.312	0.254	0.381	0.191
SPOT-RNA-2D-Single	0.734	0.876	0.631	0.727	0.878	0.620	0.755	0.942	0.630	0.747	0.909	0.634	0.779	0.902	0.685	0.750	0.890	0.647
SPOT-RNA-2D	0.819	0.893	0.757	0.754	0.870	0.665	0.768	0.923	0.657	0.793	0.921	0.696	0.853	0.909	0.803	0.773	0.888	0.684
Reduced test sets
RNAContact	0.714	0.848	0.616	0.721	0.853	0.625	0.581	0.968	0.415	0.671	0.880	0.542	0.737	0.846	0.653	0.715	0.855	0.615
SPOT-RNA-2D-Single	0.736	0.871	0.637	0.727	0.835	0.644	0.753	0.941	0.627	0.766	0.930	0.651	0.779	0.902	0.685	0.763	0.862	0.684
SPOT-RNA-2D	0.844	0.894	0.800	0.745	0.801	0.696	0.765	0.921	0.654	0.818	0.937	0.725	0.853	0.909	0.803	0.772	0.857	0.702

Note: Bold indicates the predictor with the best performance.