CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(20)		CMfinder(20)
MCC	0.662	>	0.521
Average MCC ± 95% Confidence Intervals	0.646 ± 0.122	>	0.514 ± 0.127
Sensitivity	0.521	>	0.366
Positive Predictive Value	0.844	>	0.748
Total TP	232	>	163
Total TN	67905	<	67962
Total FP	54	<	61
Total FP CONTRA	3	<	4
Total FP INCONS	40	<	51
Total FP COMP	11	>	6
Total FN	213	<	282
P-value	1.1568170475e-08

Comparison of performance of RNAalifold(20) and CMfinder(20). 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 RNAalifold(20) and CMfinder(20)).
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 RNAalifold(20) and CMfinder(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and CMfinder(20). 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 RNAalifold(20) and CMfinder(20)).

Total Scores
MCC	0.662
Average MCC ± 95% Confidence Intervals	0.646 ± 0.122
Sensitivity	0.521
Positive Predictive Value	0.844
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	0	0	0	0	9
3J2L_3	5S_rRNA links to Rfam database...	0.69	0.47	1.00	25	7850	2	0	0	2	28
3J3D_C	tRNA links to Rfam database...	0.80	0.68	0.95	19	2755	1	0	1	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.23	0.15	0.36	5	7489	9	1	8	0	28
3J3E_7	5S_rRNA links to Rfam database...	0.69	0.56	0.86	30	7105	5	1	4	0	24
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.39	0.58	14	12222	17	1	9	7	22
3J3F_7	5S_rRNA links to Rfam database...	0.74	0.58	0.94	29	7229	2	0	2	0	21
3J3V_B	5S_rRNA links to Rfam database...	0.65	0.49	0.88	28	6989	4	0	4	0	29
3ZEX_D	5S_rRNA links to Rfam database...	0.80	0.69	0.92	34	6984	3	0	3	0	15
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	11	0	9	2	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.53	1.00	17	3469	0	0	0	0	15

Total Scores
MCC	0.521
Average MCC ± 95% Confidence Intervals	0.514 ± 0.127
Sensitivity	0.366
Positive Predictive Value	0.748
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.75	0.57	1.00	17	2833	1	0	0	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.45	0.32	0.63	17	7848	11	1	9	1	36
3J3D_C	tRNA links to Rfam database...	0.76	0.61	0.94	17	2757	1	0	1	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.06	0.17	2	7491	10	1	9	0	31
3J3E_7	5S_rRNA links to Rfam database...	0.62	0.46	0.83	25	7110	5	1	4	0	29
3J3F_8	5_8S_rRNA links to Rfam database...	0.45	0.33	0.60	12	12226	8	1	7	0	24
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.52	0.84	26	7229	6	0	5	1	24
3J3V_B	5S_rRNA links to Rfam database...	0.38	0.21	0.71	12	7004	5	0	5	0	45
3ZEX_D	5S_rRNA links to Rfam database...	0.58	0.39	0.86	19	6999	3	0	3	0	30
3ZND_W	tRNA links to Rfam database...	0.45	0.39	0.53	9	2986	11	0	8	3	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.47	0.22	1.00	7	3479	0	0	0	0	25

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