CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		Cylofold
MCC	0.781	>	0.738
Average MCC ± 95% Confidence Intervals	0.780 ± 0.078	>	0.751 ± 0.069
Sensitivity	0.804	>	0.722
Positive Predictive Value	0.767	>	0.764
Total TP	864	>	775
Total TN	57618	<	57731
Total FP	392	>	326
Total FP CONTRA	77	>	65
Total FP INCONS	186	>	174
Total FP COMP	129	>	87
Total FN	210	<	299
P-value	3.56938820447e-08

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Performance plots

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

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	864
Total TN	57618
Total FP	392
Total FP CONTRA	77
Total FP INCONS	186
Total FP COMP	129
Total FN	210

Total Scores
MCC	0.781
Average MCC ± 95% Confidence Intervals	0.780 ± 0.078
Sensitivity	0.804
Positive Predictive Value	0.767
Nr of predictions	62

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2. Individual counts for ProbKnot [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.82	0.87	0.77	20	1998	15	6	0	9	3
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	0.87	0.88	0.88	7	141	1	0	1	0	1
2KZL_A	-	1.00	1.00	1.00	13	507	2	0	0	2	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LA5_A	-	0.85	0.86	0.86	6	268	3	0	1	2	1
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
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
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.89	0.86	0.93	25	2413	9	0	2	7	4
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	26	0	6	20	3
2XQD_Y	tRNA links to Rfam database...	1.00	1.00	1.00	21	1108	2	0	0	2	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.25	0.26	0.26	9	2011	26	1	24	1	26
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_X	-	0.53	0.57	0.50	4	536	7	1	3	3	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
3AKZ_H	tRNA links to Rfam database...	0.87	1.00	0.77	20	1101	9	6	0	3	0
3AM1_B	-	0.82	0.86	0.78	25	1434	7	3	4	0	4
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	9	0	5	4	4
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.91	0.89	32	2604	7	0	4	3	3
3J0L_2	-	0.30	0.31	0.31	8	2224	27	1	17	9	18
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_h	-	0.89	0.88	0.90	28	2109	3	0	3	0	4
3J0L_g	-	-0.02	0.00	0.00	0	171	7	1	4	2	2
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_a	-	0.60	0.64	0.58	7	399	6	4	1	1	4
3J16_L	tRNA links to Rfam database...	0.42	0.48	0.38	10	1133	16	3	13	0	11
3NDB_M	-	0.94	0.93	0.95	41	3671	8	0	2	6	3
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	-0.02	0.00	0.00	0	207	11	6	3	2	3
3O58_2	5S_rRNA links to Rfam database...	0.91	0.94	0.88	29	2721	10	0	4	6	2
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.29	11	4726	42	10	17	15	11
3OVB_D	-	1.00	1.00	1.00	11	215	2	0	0	2	0
3OVS_D	-	1.00	1.00	1.00	12	204	1	0	0	1	0
3P22_G	-	1.00	1.00	1.00	11	301	1	0	0	1	0
3PDR_A	ykoK links to Rfam database...	0.88	0.92	0.85	46	4786	10	5	3	2	4
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	142	0	0	0	0	0
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3UZL_B	tRNA links to Rfam database...	0.92	1.00	0.84	16	1274	11	3	0	8	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7

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Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	775
Total TN	57731
Total FP	326
Total FP CONTRA	65
Total FP INCONS	174
Total FP COMP	87
Total FN	299

Total Scores
MCC	0.738
Average MCC ± 95% Confidence Intervals	0.751 ± 0.069
Sensitivity	0.722
Positive Predictive Value	0.764
Nr of predictions	62

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2. Individual counts for Cylofold [ download as .csv ]

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
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	0.78	0.63	1.00	5	144	0	0	0	0	3
2KZL_A	-	0.83	0.69	1.00	9	511	1	0	0	1	4
2L1F_A	Gammaretro_CES links to Rfam database...	0.93	0.87	1.00	20	743	0	0	0	0	3
2L1F_B	Gammaretro_CES links to Rfam database...	0.93	0.88	1.00	21	770	0	0	0	0	3
2L2K_A	-	0.87	0.76	1.00	13	336	0	0	0	0	4
2L3C_B	-	0.84	0.71	1.00	10	229	0	0	0	0	4
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	0.95	0.90	1.00	27	958	0	0	0	0	3
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LA5_A	-	0.77	0.71	0.83	5	269	1	0	1	0	2
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
2LDL_A	-	0.81	0.67	1.00	6	134	0	0	0	0	3
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.56	0.55	0.57	16	2412	13	4	8	1	13
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.41	0.55	0.32	6	1816	25	9	4	12	5
2XQD_Y	tRNA links to Rfam database...	0.89	0.95	0.83	20	1105	5	4	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.11	0.11	4	2009	32	2	30	0	31
2Y9C_V	-	0.72	0.72	0.72	13	888	8	0	5	3	5
2YIE_X	-	0.43	0.57	0.33	4	532	10	2	6	2	3
2YIE_Z	-	-0.02	0.00	0.00	0	591	11	5	6	0	8
3AKZ_H	tRNA links to Rfam database...	0.77	0.75	0.79	15	1108	7	0	4	3	5
3AM1_B	-	0.83	0.76	0.92	22	1442	2	0	2	0	7
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	7	0	4	3	6
3J0L_2	-	0.49	0.46	0.52	12	2227	18	0	11	7	14
3J0L_7	-	0.41	0.50	0.36	5	505	10	3	6	1	5
3J0L_h	-	0.55	0.50	0.62	16	2114	10	2	8	0	16
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3NDB_M	-	0.68	0.64	0.74	28	3676	14	2	8	4	16
3NKB_B	-	0.46	0.42	0.53	8	720	7	0	7	0	11
3NMU_E	-	0.28	0.33	0.25	1	212	6	1	2	3	2
3O58_2	5S_rRNA links to Rfam database...	0.90	0.84	0.96	26	2727	3	0	1	2	5
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	30	9	11	10	11
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	0	0	0	0	0
3PDR_A	ykoK links to Rfam database...	0.86	0.78	0.95	39	4799	4	1	1	2	11
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
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
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	0.63	0.42	1.00	5	149	0	0	0	0	7
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.45	0.50	0.42	8	1274	18	4	7	7	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
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

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

Table of contents:

Overview

Performance plots

Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

2. Individual counts for ProbKnot [ download as .csv ]

Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

2. Individual counts for Cylofold [ download as .csv ]