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		RDfolder
MCC	0.729	>	0.579
Average MCC ± 95% Confidence Intervals	0.736 ± 0.056	>	0.605 ± 0.075
Sensitivity	0.635	>	0.480
Positive Predictive Value	0.844	>	0.709
Total TP	1085	>	820
Total TN	135657	<	135786
Total FP	248	<	361
Total FP CONTRA	31	<	36
Total FP INCONS	169	<	300
Total FP COMP	48	>	25
Total FN	624	<	889
P-value	3.56938820447e-08

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Performance plots

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

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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	1085
Total TN	135657
Total FP	248
Total FP CONTRA	31
Total FP INCONS	169
Total FP COMP	48
Total FN	624

Total Scores
MCC	0.729
Average MCC ± 95% Confidence Intervals	0.736 ± 0.056
Sensitivity	0.635
Positive Predictive Value	0.844
Nr of predictions	86

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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
2KD8_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KMJ_A	-	1.00	1.00	1.00	11	367	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KU0_A	-	0.47	0.31	0.71	5	696	2	0	2	0	11
2KUR_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.92	0.86	1.00	18	1110	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.93	0.86	1.00	19	1109	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
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_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	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
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
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
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LU0_A	-	0.93	0.88	1.00	14	1162	0	0	0	0	2
2RPT_A	-	1.00	1.00	1.00	7	183	0	0	0	0	0
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2WW9_D	-	0.29	0.12	0.75	3	1949	1	0	1	0	23
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_E	-	0.00	0.00	0.00	0	561	0	0	0	0	14
2WWQ_V	tRNA links to Rfam database...	0.80	0.68	0.95	19	2906	3	0	1	2	9
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
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
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
2ZZM_B	tRNA links to Rfam database...	0.18	0.16	0.23	5	3464	17	3	14	0	27
2ZZN_D	tRNA links to Rfam database...	0.82	0.78	0.88	21	2461	3	0	3	0	6
3A2K_C	tRNA links to Rfam database...	0.44	0.43	0.46	12	2900	14	2	12	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
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
3GX2_A	SAM links to Rfam database...	0.79	0.63	1.00	25	4346	1	0	0	1	15
3IAB_R	-	0.86	0.86	0.86	12	1021	4	1	1	2	2
3ID5_D	-	-0.01	0.00	0.00	0	490	6	3	3	0	9
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.80	0.67	0.96	22	4255	1	0	1	0	11
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.41	0.31	0.56	5	1119	4	2	2	0	11
3J16_L	tRNA links to Rfam database...	0.50	0.40	0.63	12	2756	7	0	7	0	18
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J3D_C	tRNA links to Rfam database...	0.49	0.43	0.57	12	2754	9	0	9	0	16
3JYV_7	tRNA links to Rfam database...	0.77	0.59	1.00	19	2831	0	0	0	0	13
3KTW_C	-	0.45	0.40	0.53	17	4528	16	2	13	1	26
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
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
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
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
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.78	0.97	31	4721	2	0	1	1	9
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
4ATO_G	-	0.31	0.20	0.50	2	524	2	0	2	0	8
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
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0
4JRC_A	-	0.81	0.70	0.94	16	1523	1	0	1	0	7

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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	820
Total TN	135786
Total FP	361
Total FP CONTRA	36
Total FP INCONS	300
Total FP COMP	25
Total FN	889

Total Scores
MCC	0.579
Average MCC ± 95% Confidence Intervals	0.605 ± 0.075
Sensitivity	0.480
Positive Predictive Value	0.709
Nr of predictions	86

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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
2KD8_A	-	0.94	0.89	1.00	8	223	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.89	0.79	1.00	15	1113	1	0	0	1	4
2KMJ_A	-	1.00	1.00	1.00	11	367	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KU0_A	-	-0.01	0.00	0.00	0	696	7	0	7	0	16
2KUR_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KUU_A	K10_TLS links to Rfam database...	0.84	0.71	1.00	15	1113	1	0	0	1	6
2KUV_A	K10_TLS links to Rfam database...	0.85	0.73	1.00	16	1112	0	0	0	0	6
2KUW_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KX8_A	7SK links to Rfam database...	0.88	0.78	1.00	14	847	0	0	0	0	4
2KXM_A	-	0.70	0.50	1.00	5	346	0	0	0	0	5
2KZL_A	-	0.78	0.74	0.82	14	1468	3	1	2	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...	-0.01	0.00	0.00	0	2067	13	2	11	0	24
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	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1526	14	2	12	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	0	0	0	0	2
2LDT_A	-	0.68	0.47	1.00	7	458	0	0	0	0	8
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LU0_A	-	-0.01	0.00	0.00	0	1172	4	0	4	0	16
2RPT_A	-	-0.03	0.00	0.00	0	186	4	1	3	0	7
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2WW9_F	-	0.71	0.60	0.86	6	293	1	0	1	0	4
2WW9_D	-	0.29	0.12	0.75	3	1949	1	0	1	0	23
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.64	0.50	0.82	14	2909	4	0	3	1	14
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4538	22	5	17	0	20
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.57	0.50	0.67	12	2260	7	1	5	1	12
2YIE_X	-	0.38	0.33	0.44	4	1369	5	1	4	0	8
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
2ZZM_B	tRNA links to Rfam database...	0.10	0.09	0.13	3	3462	21	1	20	0	29
2ZZN_D	tRNA links to Rfam database...	0.84	0.78	0.91	21	2462	2	0	2	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3A3A_A	tRNA-Sec links to Rfam database...	0.53	0.41	0.71	15	3634	6	0	6	0	22
3ADB_C	-	0.46	0.39	0.54	15	4158	13	0	13	0	23
3AKZ_H	tRNA links to Rfam database...	0.48	0.43	0.55	12	2679	11	1	9	1	16
3AM1_B	-	0.47	0.43	0.54	15	3212	13	1	12	0	20
3AMU_B	tRNA links to Rfam database...	0.18	0.15	0.22	4	2985	16	2	12	2	23
3GX2_A	SAM links to Rfam database...	0.50	0.40	0.64	16	4346	10	1	8	1	24
3IAB_R	-	0.86	0.86	0.86	12	1021	4	1	1	2	2
3ID5_D	-	-0.01	0.00	0.00	0	490	6	3	3	0	9
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.00	0.00	0.00	0	4268	10	0	10	0	33
3J0L_a	-	-0.01	0.00	0.00	0	1124	4	1	3	0	16
3J0L_8	-	0.86	0.75	1.00	6	184	0	0	0	0	2
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3J20_0	tRNA links to Rfam database...	0.73	0.57	0.94	17	2832	2	0	1	1	13
3J3D_C	tRNA links to Rfam database...	0.72	0.61	0.85	17	2755	3	0	3	0	11
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3KTW_C	-	0.08	0.07	0.12	3	4535	23	0	22	1	40
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NKB_B	-	0.37	0.31	0.47	8	1999	9	0	9	0	18
3NMU_E	-	0.41	0.17	1.00	1	560	3	0	0	3	5
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	-	0.91	0.83	1.00	10	731	0	0	0	0	2
3R4F_A	-	0.76	0.68	0.85	17	2125	3	1	2	0	8
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...	0.30	0.17	0.54	7	3903	6	0	6	0	35
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
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	0	0	0	0	1
3TS0_U	-	0.91	0.83	1.00	5	248	0	0	0	0	1
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.27	0.23	0.33	9	4726	18	1	17	0	31
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	-	0.63	0.40	1.00	4	524	0	0	0	0	6
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0
4JRC_A	-	0.81	0.65	1.00	15	1525	0	0	0	0	8

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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 RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

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