CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CRWrnafold		Alterna
MCC	0.673	>	0.669
Average MCC ± 95% Confidence Intervals	0.682 ± 0.199	<	0.689 ± 0.172
Sensitivity	0.690	=	0.690
Positive Predictive Value	0.674	>	0.665
Total TP	149	=	149
Total TN	8049	>	8046
Total FP	88	<	96
Total FP CONTRA	22	=	22
Total FP INCONS	50	<	53
Total FP COMP	16	<	21
Total FN	67	=	67
P-value	0.00148397846487

Comparison of performance of CRWrnafold and Alterna. 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 CRWrnafold and Alterna).
Comparison of performance of CRWrnafold and Alterna. 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 CRWrnafold and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for CRWrnafold and Alterna. 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 CRWrnafold and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for CRWrnafold and Alterna. 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 CRWrnafold and Alterna).

Total Scores
MCC	0.673
Average MCC ± 95% Confidence Intervals	0.682 ± 0.199
Sensitivity	0.690
Positive Predictive Value	0.674
Nr of predictions	19

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2LDL_A	-	0.94	0.89	1.00	8	132	1	0	0	1	1
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.53	0.57	0.50	4	536	9	1	3	5	3
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J0L_a	-	0.39	0.36	0.44	4	402	6	3	2	1	7
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J16_L	tRNA links to Rfam database...	1.00	1.00	1.00	21	1138	0	0	0	0	0
3SD1_A	THF links to Rfam database...	0.63	0.66	0.61	19	1502	12	6	6	0	10
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	0	0	0	0	0
3TS0_U	-	1.00	1.00	1.00	6	112	0	0	0	0	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0

Total Scores
MCC	0.669
Average MCC ± 95% Confidence Intervals	0.689 ± 0.172
Sensitivity	0.690
Positive Predictive Value	0.665
Nr of predictions	19

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.47	0.44	0.53	8	513	7	0	7	0	10
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.53	0.57	0.50	4	536	9	1	3	5	3
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	4
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.63	0.62	0.67	8	472	8	0	4	4	5
3J0L_7	-	0.37	0.40	0.36	4	508	9	2	5	2	6
3J0L_g	-	-0.02	0.00	0.00	0	169	9	3	4	2	2
3J16_L	tRNA links to Rfam database...	0.76	0.76	0.76	16	1138	5	3	2	0	5
3SD1_A	THF links to Rfam database...	0.55	0.55	0.57	16	1505	12	4	8	0	13
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	144	0	0	0	0	2
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0

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