CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Cylofold		RDfolder
MCC	0.796	>	0.662
Average MCC ± 95% Confidence Intervals	0.776 ± 0.079	>	0.680 ± 0.103
Sensitivity	0.773	>	0.627
Positive Predictive Value	0.830	>	0.715
Total TP	545	>	442
Total TN	27080	<	27119
Total FP	154	<	201
Total FP CONTRA	34	<	43
Total FP INCONS	78	<	133
Total FP COMP	42	>	25
Total FN	160	<	263
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Cylofold - scored higher in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	545
Total TN	27080
Total FP	154
Total FP CONTRA	34
Total FP INCONS	78
Total FP COMP	42
Total FN	160

Total Scores
MCC	0.796
Average MCC ± 95% Confidence Intervals	0.776 ± 0.079
Sensitivity	0.773
Positive Predictive Value	0.830
Nr of predictions	48

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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
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_B	Gammaretro_CES links to Rfam database...	0.93	0.88	1.00	21	770	0	0	0	0	3
2L1F_A	Gammaretro_CES links to Rfam database...	0.93	0.87	1.00	20	743	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
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	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...	0.41	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
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
3ADB_C	-	0.84	0.82	0.87	27	1788	4	0	4	0	6
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
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_7	-	0.41	0.50	0.36	5	505	10	3	6	1	5
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
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
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
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
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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Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	442
Total TN	27119
Total FP	201
Total FP CONTRA	43
Total FP INCONS	133
Total FP COMP	25
Total FN	263

Total Scores
MCC	0.662
Average MCC ± 95% Confidence Intervals	0.680 ± 0.103
Sensitivity	0.627
Positive Predictive Value	0.715
Nr of predictions	48

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.93	0.88	1.00	14	357	0	0	0	0	2
2KXM_A	-	0.78	0.63	1.00	5	144	0	0	0	0	3
2KZL_A	-	1.00	1.00	1.00	13	507	4	0	0	4	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	-0.02	0.00	0.00	0	750	13	2	11	0	23
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	-	0.77	0.71	0.83	5	269	1	0	1	0	2
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	514	14	3	11	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LDT_A	-	0.79	0.64	1.00	7	155	0	0	0	0	4
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	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...	-0.01	0.00	0.00	0	1813	22	10	12	0	11
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2Y9C_V	-	0.68	0.67	0.71	12	889	7	0	5	2	6
2YIE_X	-	0.57	0.57	0.57	4	537	5	0	3	2	3
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
3ADB_C	-	0.48	0.45	0.54	15	1791	13	1	12	0	18
3AKZ_H	tRNA links to Rfam database...	0.53	0.55	0.52	11	1106	12	1	9	2	9
3AM1_B	-	0.52	0.52	0.54	15	1438	13	4	9	0	14
3AMU_B	tRNA links to Rfam database...	0.20	0.21	0.22	4	1139	16	4	10	2	15
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
3J0L_g	-	-0.01	0.00	0.00	0	173	3	2	1	0	2
3J0L_7	-	-0.01	0.00	0.00	0	514	5	1	4	0	10
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J16_L	tRNA links to Rfam database...	0.26	0.24	0.31	5	1143	11	0	11	0	16
3NKB_B	-	0.43	0.42	0.47	8	718	9	2	7	0	11
3NMU_E	-	0.57	0.33	1.00	1	215	3	0	0	3	2
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	-	0.95	0.91	1.00	10	302	0	0	0	0	1
3R4F_A	-	0.78	0.73	0.84	16	887	4	2	1	1	6
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...	0.35	0.24	0.54	7	1520	6	1	5	0	22
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
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
3TS2_V	-	1.00	1.00	1.00	5	103	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...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9

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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 Cylofold - scored higher in this pairwise comparison

1. Total counts & total scores for Cylofold

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

Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

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