CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CRWrnafold		Pknots
MCC	0.467	>	0.430
Average MCC ± 95% Confidence Intervals	0.424 ± 0.161	<	0.445 ± 0.155
Sensitivity	0.410	>	0.391
Positive Predictive Value	0.540	>	0.481
Total TP	177	>	169
Total TN	55098	>	55075
Total FP	167	<	200
Total FP CONTRA	18	=	18
Total FP INCONS	133	<	164
Total FP COMP	16	<	18
Total FN	255	<	263
P-value	2.15570126439e-07

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

Total Scores
MCC	0.467
Average MCC ± 95% Confidence Intervals	0.424 ± 0.161
Sensitivity	0.410
Positive Predictive Value	0.540
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LKR_A	-	0.52	0.44	0.63	17	6078	12	2	8	2	22
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.39	0.31	0.50	5	1118	5	1	4	0	11
3J0L_2	-	0.25	0.24	0.28	8	6187	23	2	19	2	25
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J16_L	tRNA links to Rfam database...	0.84	0.70	1.00	21	2754	0	0	0	0	9
3SD1_A	THF links to Rfam database...	0.52	0.45	0.61	19	3885	12	2	10	0	23
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.13	5	11741	44	4	31	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	20	4344	8	2	5	1	22
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1313	2	1	1	0	8

Total Scores
MCC	0.430
Average MCC ± 95% Confidence Intervals	0.445 ± 0.155
Sensitivity	0.391
Positive Predictive Value	0.481
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.79	0.75	0.83	15	1522	3	1	2	0	5
2LKR_A	-	0.44	0.44	0.45	17	6067	22	4	17	1	22
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3J0L_g	-	-0.01	0.00	0.00	0	460	5	2	3	0	4
3J0L_a	-	0.35	0.31	0.42	5	1116	7	1	6	0	11
3J0L_2	-	0.36	0.36	0.36	12	6183	23	3	18	2	21
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J16_L	tRNA links to Rfam database...	0.34	0.30	0.41	9	2753	13	0	13	0	21
3SD1_A	THF links to Rfam database...	0.65	0.52	0.81	22	3889	5	0	5	0	20
3U4M_B	-	0.26	0.22	0.32	8	3135	17	0	17	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.25	8	11749	36	3	21	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4ENB_A	crcB links to Rfam database...	0.83	0.79	0.88	15	1258	2	1	1	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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