CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidFold		Cylofold
MCC	0.711	>	0.648
Average MCC ± 95% Confidence Intervals	0.727 ± 0.061	>	0.676 ± 0.066
Sensitivity	0.615	>	0.559
Positive Predictive Value	0.827	>	0.758
Total TP	910	>	827
Total TN	155205	<	155215
Total FP	239	<	305
Total FP CONTRA	18	<	36
Total FP INCONS	173	<	228
Total FP COMP	48	>	41
Total FN	570	<	653
P-value	3.56938820447e-08

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Performance plots

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

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Performance of CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	910
Total TN	155205
Total FP	239
Total FP CONTRA	18
Total FP INCONS	173
Total FP COMP	48
Total FN	570

Total Scores
MCC	0.711
Average MCC ± 95% Confidence Intervals	0.727 ± 0.061
Sensitivity	0.615
Positive Predictive Value	0.827
Nr of predictions	63

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2. Individual counts for CentroidFold [ 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...	0.92	0.90	0.95	18	971	1	0	1	0	2
2LA5_A	-	0.42	0.26	0.71	5	623	2	0	2	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.49	0.35	0.70	7	1530	3	1	2	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	-	0.82	0.74	0.91	29	6073	4	0	3	1	10
2LWK_A	-	0.92	0.92	0.92	12	483	1	0	1	0	1
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	25	0	9	16	10
2XQD_Y	tRNA links to Rfam database...	0.75	0.67	0.86	18	2829	3	0	3	0	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.15	0.12	0.20	5	5126	20	1	19	0	37
2Y9C_V	-	0.66	0.63	0.71	15	2257	8	1	5	2	9
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
2YIE_X	-	0.67	0.58	0.78	7	1369	3	1	1	1	5
3ADB_C	-	0.92	0.84	1.00	32	4154	0	0	0	0	6
3AKZ_H	tRNA links to Rfam database...	0.43	0.39	0.48	11	2678	12	2	10	0	17
3AM1_B	-	0.68	0.63	0.73	22	3210	8	1	7	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...	0.68	0.61	0.77	33	6860	10	1	9	0	21
3J0L_h	-	0.77	0.65	0.90	28	6074	5	0	3	2	15
3J0L_2	-	0.25	0.24	0.28	8	6187	24	0	21	3	25
3J0L_a	-	0.41	0.31	0.56	5	1119	4	2	2	0	11
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J16_L	tRNA links to Rfam database...	0.50	0.40	0.63	12	2756	7	0	7	0	18
3NDB_M	-	0.80	0.70	0.91	43	9133	5	0	4	1	18
3NKB_B	-	0.57	0.50	0.65	13	1996	7	0	7	0	13
3NMU_E	-	0.71	0.50	1.00	3	558	3	0	0	3	3
3O58_2	5S_rRNA links to Rfam database...	0.82	0.76	0.88	29	7227	7	1	3	3	9
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.29	0.50	10	12383	10	0	10	0	25
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	1	0	0	1	1
3PDR_A	ykoK links to Rfam database...	0.73	0.60	0.90	43	12832	7	0	5	2	29
3R4F_A	-	0.81	0.76	0.86	19	2123	3	1	2	0	6
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...	0.58	0.48	0.71	20	3888	8	1	7	0	22
3SIU_F	-	0.79	0.64	1.00	7	371	0	0	0	0	4
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	1	0	0	1	1
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.57	0.46	0.71	17	3136	7	0	7	0	20
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.45	0.33	0.61	14	4348	10	1	8	1	28
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...	0.73	0.58	0.92	11	1314	1	1	0	0	8

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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	827
Total TN	155215
Total FP	305
Total FP CONTRA	36
Total FP INCONS	228
Total FP COMP	41
Total FN	653

Total Scores
MCC	0.648
Average MCC ± 95% Confidence Intervals	0.676 ± 0.066
Sensitivity	0.559
Positive Predictive Value	0.758
Nr of predictions	63

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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_h	-	0.48	0.37	0.62	16	6079	10	0	10	0	27
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_a	-	0.22	0.19	0.27	3	1117	8	1	7	0	13
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
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
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
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_2	5S_rRNA links to Rfam database...	0.80	0.68	0.93	26	7232	3	0	2	1	12
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
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
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
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

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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 CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

2. Individual counts for CentroidFold [ 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 ]