CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(20)		RNASLOpt
MCC	0.606	>	0.464
Average MCC ± 95% Confidence Intervals	0.606 ± 0.116	>	0.492 ± 0.139
Sensitivity	0.502	>	0.387
Positive Predictive Value	0.737	>	0.562
Total TP	316	>	244
Total TN	103745	>	103740
Total FP	156	<	237
Total FP CONTRA	10	<	21
Total FP INCONS	103	<	169
Total FP COMP	43	<	47
Total FN	314	<	386
P-value	3.30280588002e-08

Comparison of performance of TurboFold(20) and RNASLOpt. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for TurboFold(20) and RNASLOpt).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for TurboFold(20) and RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(20) and RNASLOpt. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for TurboFold(20) and RNASLOpt).

Total Scores
MCC	0.606
Average MCC ± 95% Confidence Intervals	0.606 ± 0.116
Sensitivity	0.502
Positive Predictive Value	0.737
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	0	5	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.74	0.58	0.94	31	7842	5	0	2	3	22
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_7	5S_rRNA links to Rfam database...	0.65	0.54	0.78	29	7103	8	1	7	0	25
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.21	5	7479	28	2	17	9	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.38	0.36	0.39	13	12213	34	2	18	14	23
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.68	0.92	34	7223	4	0	3	1	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	14	14171	14	2	9	3	38
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.63	0.91	31	6987	3	0	3	0	18
3ZND_W	tRNA links to Rfam database...	0.43	0.39	0.47	9	2984	12	1	9	2	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	28	0	19	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11

Total Scores
MCC	0.464
Average MCC ± 95% Confidence Intervals	0.492 ± 0.139
Sensitivity	0.387
Positive Predictive Value	0.562
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_7	5S_rRNA links to Rfam database...	0.48	0.35	0.66	19	7111	10	0	10	0	35
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	30	1	19	10	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.35	12	12212	35	3	19	13	24
3J3F_7	5S_rRNA links to Rfam database...	0.18	0.16	0.22	8	7224	28	1	27	0	42
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.21	0.33	11	14163	35	2	20	13	41
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.59	0.97	29	6991	1	0	1	0	20
3ZND_W	tRNA links to Rfam database...	0.21	0.22	0.22	5	2980	20	1	17	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.