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		Vsfold5
MCC	0.699	>	0.592
Average MCC ± 95% Confidence Intervals	0.729 ± 0.065	>	0.647 ± 0.083
Sensitivity	0.685	>	0.592
Positive Predictive Value	0.723	>	0.604
Total TP	948	>	820
Total TN	84949	>	84903
Total FP	465	<	607
Total FP CONTRA	101	<	148
Total FP INCONS	263	<	390
Total FP COMP	101	>	69
Total FN	436	<	564
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Cylofold and Vsfold5. 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 Vsfold5).
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 Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold and Vsfold5. 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 Vsfold5).

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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	948
Total TN	84949
Total FP	465
Total FP CONTRA	101
Total FP INCONS	263
Total FP COMP	101
Total FN	436

Total Scores
MCC	0.699
Average MCC ± 95% Confidence Intervals	0.729 ± 0.065
Sensitivity	0.685
Positive Predictive Value	0.723
Nr of predictions	73

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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_Z	-	-0.02	0.00	0.00	0	591	11	5	6	0	8
2YIE_X	-	0.43	0.57	0.33	4	532	10	2	6	2	3
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
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	7	0	4	3	6
3J0L_h	-	0.55	0.50	0.62	16	2114	10	2	8	0	16
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
3J0L_2	-	0.49	0.46	0.52	12	2227	18	0	11	7	14
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
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_1	tRNA links to Rfam database...	0.71	0.75	0.68	15	1090	8	2	5	1	5
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J2C_O	-	0.51	0.49	0.54	20	3950	19	1	16	2	21
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
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
3W3S_B	tRNA-Sec links to Rfam database...	0.48	0.45	0.52	15	1960	15	1	13	1	18
3ZEX_E	-	0.00	0.00	0.00	0	8258	51	15	31	5	34
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.69	0.71	24	2762	11	5	5	1	11
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
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

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Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	820
Total TN	84903
Total FP	607
Total FP CONTRA	148
Total FP INCONS	390
Total FP COMP	69
Total FN	564

Total Scores
MCC	0.592
Average MCC ± 95% Confidence Intervals	0.647 ± 0.083
Sensitivity	0.592
Positive Predictive Value	0.604
Nr of predictions	73

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2. Individual counts for Vsfold5 [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.71	0.78	0.64	18	1996	13	8	2	3	5
2KX8_A	7SK links to Rfam database...	0.97	0.94	1.00	15	356	0	0	0	0	1
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	1	0	0	1	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.70	0.61	0.82	14	746	3	0	3	0	9
2L1F_B	Gammaretro_CES links to Rfam database...	0.71	0.63	0.83	15	773	3	0	3	0	9
2L2K_A	-	0.94	0.88	1.00	15	334	0	0	0	0	2
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...	0.93	0.87	1.00	26	959	0	0	0	0	4
2L5Z_A	-	0.68	0.67	0.75	6	103	2	0	2	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.94	1.00	17	340	1	0	0	1	1
2LA5_A	-	-0.03	0.00	0.00	0	268	7	0	7	0	7
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	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
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LK3_A	-	0.94	0.89	1.00	8	92	0	0	0	0	1
2LKR_A	-	0.31	0.31	0.32	9	2412	19	5	14	0	20
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...	-0.01	0.00	0.00	0	1803	32	17	15	0	11
2XQD_Y	tRNA links to Rfam database...	0.95	0.90	1.00	19	1110	1	0	0	1	2
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.02	0.00	0.00	0	2014	31	2	29	0	35
2Y9C_V	-	0.74	0.72	0.76	13	889	7	0	4	3	5
2YIE_Z	-	-0.02	0.00	0.00	0	591	11	5	6	0	8
2YIE_X	-	0.43	0.57	0.33	4	532	10	2	6	2	3
3ADB_C	-	0.72	0.61	0.87	20	1796	3	0	3	0	13
3AKZ_H	tRNA links to Rfam database...	0.97	0.95	1.00	19	1108	1	0	0	1	1
3AM1_B	-	0.86	0.86	0.86	25	1437	4	3	1	0	4
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	5	0	4	1	6
3J0L_h	-	0.20	0.19	0.24	6	2115	19	3	16	0	26
3J0L_1	-	0.25	0.23	0.30	3	474	8	3	4	1	10
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3J0L_2	-	0.42	0.42	0.44	11	2225	21	1	13	7	15
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J16_L	tRNA links to Rfam database...	0.98	0.95	1.00	20	1139	0	0	0	0	1
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	7	0	5	2	5
3J20_0	tRNA links to Rfam database...	0.76	0.76	0.76	16	1198	6	3	2	1	5
3J2C_O	-	0.33	0.32	0.36	13	3951	26	3	20	3	28
3J2L_3	5S_rRNA links to Rfam database...	0.70	0.71	0.71	24	2986	13	3	7	3	10
3NDB_M	-	0.07	0.07	0.08	3	3678	33	2	31	0	41
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	0.28	0.33	0.25	1	212	5	2	1	2	2
3O58_2	5S_rRNA links to Rfam database...	0.50	0.52	0.50	16	2722	19	3	13	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.59	0.45	13	4735	28	11	5	12	9
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...	0.69	0.64	0.74	32	4797	13	3	8	2	18
3R4F_A	-	0.98	0.95	1.00	21	885	1	0	0	1	1
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25
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	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...	0.24	0.31	0.20	5	1268	20	9	11	0	11
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.83	0.85	0.82	28	1955	7	2	4	1	5
3ZEX_E	-	0.11	0.15	0.09	5	8247	54	21	31	2	29
3ZEX_D	5S_rRNA links to Rfam database...	0.09	0.09	0.12	3	2771	24	5	17	2	32
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.21	0.21	0.25	6	1413	19	2	16	1	23
4ATO_G	-	0.67	0.86	0.55	6	209	5	5	0	0	1
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...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.15	0.14	0.17	4	1825	19	3	16	0	24

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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 Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ download as .csv ]