CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		RNAshapes
MCC	0.669	>	0.627
Average MCC ± 95% Confidence Intervals	0.663 ± 0.123	>	0.592 ± 0.101
Sensitivity	0.648	>	0.625
Positive Predictive Value	0.700	>	0.640
Total TP	282	>	272
Total TN	27820	>	27798
Total FP	145	<	189
Total FP CONTRA	41	>	39
Total FP INCONS	80	<	114
Total FP COMP	24	<	36
Total FN	153	<	163
P-value	2.57237423209e-08

Comparison of performance of Cylofold and RNAshapes. 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 Cylofold and RNAshapes).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold and RNAshapes. 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 Cylofold and RNAshapes).

Total Scores
MCC	0.669
Average MCC ± 95% Confidence Intervals	0.663 ± 0.123
Sensitivity	0.648
Positive Predictive Value	0.700
Nr of predictions	19

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.85	0.87	0.83	20	2000	12	4	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
3ADB_C	-	0.84	0.82	0.87	27	1788	4	0	4	0	6
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3NKB_B	-	0.46	0.42	0.53	8	720	7	0	7	0	11
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	30	9	11	10	11
3PDR_A	ykoK links to Rfam database...	0.86	0.78	0.95	39	4799	4	1	1	2	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.48	0.45	0.52	15	1960	15	1	13	1	18
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ATO_G	-	0.88	1.00	0.78	7	211	2	2	0	0	0
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.23	0.18	0.31	5	1832	11	7	4	0	23

Total Scores
MCC	0.627
Average MCC ± 95% Confidence Intervals	0.592 ± 0.101
Sensitivity	0.625
Positive Predictive Value	0.640
Nr of predictions	19

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
2M58_A	-	0.40	0.42	0.42	5	532	7	1	6	0	7
3ADB_C	-	0.71	0.70	0.74	23	1788	8	0	8	0	10
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3NKB_B	-	0.75	0.74	0.78	14	717	6	0	4	2	5
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3PDR_A	ykoK links to Rfam database...	0.80	0.80	0.80	40	4790	12	3	7	2	10
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.58	0.63	19	1959	12	2	9	1	14
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12

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