CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Sfold		Cylofold
MCC	0.657	>	0.607
Average MCC ± 95% Confidence Intervals	0.696 ± 0.060	>	0.658 ± 0.061
Sensitivity	0.563	>	0.517
Positive Predictive Value	0.772	>	0.718
Total TP	1079	>	990
Total TN	222659	<	222679
Total FP	376	<	437
Total FP CONTRA	30	<	44
Total FP INCONS	289	<	344
Total FP COMP	57	>	49
Total FN	836	<	925
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	1079
Total TN	222659
Total FP	376
Total FP CONTRA	30
Total FP INCONS	289
Total FP COMP	57
Total FN	836

Total Scores
MCC	0.657
Average MCC ± 95% Confidence Intervals	0.696 ± 0.060
Sensitivity	0.563
Positive Predictive Value	0.772
Nr of predictions	75

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.89	0.80	1.00	8	343	0	0	0	0	2
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.94	0.88	1.00	30	2455	0	0	0	0	4
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.45	0.35	0.58	7	1528	5	0	5	0	13
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.89	0.79	1.00	31	6074	1	0	0	1	8
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2RRC_A	-	0.83	0.70	1.00	7	224	0	0	0	0	3
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	23	0	9	14	10
2XQD_Y	tRNA links to Rfam database...	0.77	0.67	0.90	18	2830	2	0	2	0	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.36	0.31	0.43	13	5121	17	1	16	0	29
2Y9C_V	-	0.65	0.63	0.68	15	2256	8	1	6	1	9
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
2YIE_X	-	0.58	0.33	1.00	4	1374	0	0	0	0	8
3ADB_C	-	0.62	0.55	0.70	21	4156	9	0	9	0	17
3AKZ_H	tRNA links to Rfam database...	0.44	0.39	0.50	11	2679	11	2	9	0	17
3AM1_B	-	0.69	0.63	0.76	22	3211	7	1	6	0	13
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	0	7	0	21
3J0L_7	-	-0.01	0.00	0.00	0	1222	3	0	3	0	17
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_a	-	0.51	0.50	0.53	8	1113	7	3	4	0	8
3J0L_2	-	0.36	0.33	0.39	11	6188	19	2	15	2	22
3J0L_1	-	0.76	0.63	0.92	12	1212	3	0	1	2	7
3J0L_h	-	0.75	0.60	0.93	26	6077	4	0	2	2	17
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
3J20_1	tRNA links to Rfam database...	0.73	0.70	0.76	16	2905	6	0	5	1	7
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J2C_O	-	0.64	0.48	0.86	30	10261	6	0	5	1	33
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3NDB_M	-	0.81	0.69	0.95	42	9136	3	0	2	1	19
3NKB_B	-	0.64	0.54	0.78	14	1998	4	0	4	0	12
3NMU_E	-	0.61	0.50	0.75	3	557	4	0	1	3	3
3O58_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	17	0	10	7	23
3O58_2	5S_rRNA links to Rfam database...	0.74	0.74	0.74	28	7222	11	3	7	1	10
3OVB_D	-	1.00	1.00	1.00	11	584	1	0	0	1	0
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	0	0	0	0	1
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.85	40	12833	9	0	7	2	32
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.65	0.50	0.84	21	3891	4	1	3	0	21
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.51	0.32	0.80	12	3555	3	2	1	0	25
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.57	0.53	0.64	21	4720	13	1	11	1	19
3ZEX_D	5S_rRNA links to Rfam database...	0.74	0.63	0.86	31	6985	5	0	5	0	18
3ZEX_E	-	0.00	0.00	0.00	0	21891	56	3	51	2	77
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.31	0.10	1.00	1	527	0	0	0	0	9
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.62	0.47	0.83	15	3468	3	1	2	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.63	0.44	0.89	16	5133	2	2	0	0	20
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0

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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	990
Total TN	222679
Total FP	437
Total FP CONTRA	44
Total FP INCONS	344
Total FP COMP	49
Total FN	925

Total Scores
MCC	0.607
Average MCC ± 95% Confidence Intervals	0.658 ± 0.061
Sensitivity	0.517
Positive Predictive Value	0.718
Nr of predictions	75

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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	-	0.72	0.60	0.86	24	5123	8	2	2	4	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.70	0.50	1.00	5	346	0	0	0	0	5
2KZL_A	-	0.72	0.53	1.00	10	1475	0	0	0	0	9
2L1F_B	Gammaretro_CES links to Rfam database...	0.92	0.84	1.00	21	2124	0	0	0	0	4
2L1F_A	Gammaretro_CES links to Rfam database...	0.91	0.83	1.00	20	2060	0	0	0	0	4
2L2K_A	-	0.82	0.68	1.00	13	848	0	0	0	0	6
2L3C_B	-	0.76	0.59	1.00	10	551	0	0	0	0	7
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.89	0.79	1.00	27	2458	0	0	0	0	7
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LDL_A	-	0.73	0.55	1.00	6	345	0	0	0	0	5
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.50	0.44	0.59	17	6076	12	2	10	0	22
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.38	0.40	0.36	8	4538	23	7	7	9	12
2XQD_Y	tRNA links to Rfam database...	0.81	0.78	0.84	21	2825	4	4	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.10	0.11	4	5115	32	1	31	0	38
2Y9C_V	-	0.59	0.54	0.65	13	2258	8	1	6	1	11
2YIE_Z	-	-0.01	0.00	0.00	0	1529	11	3	8	0	12
2YIE_X	-	0.30	0.33	0.29	4	1364	10	2	8	0	8
3ADB_C	-	0.78	0.71	0.87	27	4155	4	0	4	0	11
3AKZ_H	tRNA links to Rfam database...	0.66	0.57	0.76	16	2680	6	0	5	1	12
3AM1_B	-	0.76	0.63	0.92	22	3216	2	0	2	0	13
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J0L_7	-	0.30	0.29	0.33	5	1210	10	0	10	0	12
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.22	0.19	0.27	3	1117	8	1	7	0	13
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_h	-	0.48	0.37	0.62	16	6079	10	0	10	0	27
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_1	tRNA links to Rfam database...	0.69	0.70	0.70	16	2903	7	2	5	0	7
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J2C_O	-	0.43	0.33	0.55	21	10258	18	0	17	1	42
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3NDB_M	-	0.58	0.48	0.71	29	9139	13	1	11	1	32
3NKB_B	-	0.40	0.31	0.53	8	2001	7	0	7	0	18
3NMU_E	-	0.20	0.17	0.25	1	557	6	1	2	3	5
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
3O58_2	5S_rRNA links to Rfam database...	0.80	0.68	0.93	26	7232	3	0	2	1	12
3OVB_D	-	1.00	1.00	1.00	11	584	1	0	0	1	0
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	0	0	0	0	1
3PDR_A	ykoK links to Rfam database...	0.72	0.54	0.95	39	12839	4	0	2	2	33
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	0.64	0.42	1.00	5	401	0	0	0	0	7
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.45	0.38	0.54	14	3544	12	1	11	0	23
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.52	15	4724	15	0	14	1	25
3ZEX_D	5S_rRNA links to Rfam database...	0.58	0.49	0.69	24	6986	11	0	11	0	25
3ZEX_E	-	0.00	0.00	0.00	0	21897	51	2	46	3	77
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ATO_G	-	0.73	0.70	0.78	7	519	2	1	1	0	3
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FNJ_A	-	0.70	0.50	1.00	8	587	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11
4FRN_A	AdoCbl-variant links to Rfam database...	0.20	0.14	0.31	5	5135	11	2	9	0	31
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	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 Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

2. Individual counts for Sfold [ 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 ]