CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(20)		RNASLOpt
MCC	0.759	>	0.635
Average MCC ± 95% Confidence Intervals	0.738 ± 0.167	>	0.657 ± 0.163
Sensitivity	0.688	>	0.616
Positive Predictive Value	0.842	>	0.662
Total TP	192	>	172
Total TN	24179	>	24147
Total FP	52	<	121
Total FP CONTRA	8	<	31
Total FP INCONS	28	<	57
Total FP COMP	16	<	33
Total FN	87	<	107
P-value	1.89649746203e-08

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

Total Scores
MCC	0.759
Average MCC ± 95% Confidence Intervals	0.738 ± 0.167
Sensitivity	0.688
Positive Predictive Value	0.842
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...	0.95	0.95	0.95	20	1198	1	1	0	0	1
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.86	0.74	1.00	25	2995	2	0	0	2	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.46	0.41	0.52	12	5351	16	2	9	5	17
3ZEX_D	5S_rRNA links to Rfam database...	0.91	0.89	0.94	31	2763	6	0	2	4	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.84	0.97	31	2731	1	0	1	0	6
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.71	1.00	17	1185	0	0	0	0	7

Total Scores
MCC	0.635
Average MCC ± 95% Confidence Intervals	0.657 ± 0.163
Sensitivity	0.616
Positive Predictive Value	0.662
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...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.74	1.00	26	2770	4	0	0	4	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4A1C_3	5S_rRNA links to Rfam database...	0.79	0.73	0.87	27	2732	5	0	4	1	10
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10

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