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		ProbKnot
MCC	0.761	>	0.741
Average MCC ± 95% Confidence Intervals	0.808 ± 0.063	>	0.784 ± 0.070
Sensitivity	0.756	<	0.774
Positive Predictive Value	0.772	>	0.715
Total TP	1041	<	1066
Total TN	115942	>	115799
Total FP	453	<	610
Total FP CONTRA	99	<	148
Total FP INCONS	208	<	277
Total FP COMP	146	<	185
Total FN	336	>	311
P-value	3.56938820447e-08

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Performance plots

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

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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	1041
Total TN	115942
Total FP	453
Total FP CONTRA	99
Total FP INCONS	208
Total FP COMP	146
Total FN	336

Total Scores
MCC	0.761
Average MCC ± 95% Confidence Intervals	0.808 ± 0.063
Sensitivity	0.756
Positive Predictive Value	0.772
Nr of predictions	74

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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	-	0.91	0.87	0.95	20	2003	9	1	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	-	1.00	1.00	1.00	8	141	0	0	0	0	0
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	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...	1.00	1.00	1.00	23	740	0	0	0	0	0
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	3	0	1	2	2
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	0	5	0	11
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.95	0.90	1.00	26	2414	6	0	0	6	3
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
2RRC_A	-	1.00	1.00	1.00	7	68	0	0	0	0	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	25	0	6	19	3
2XQD_Y	tRNA links to Rfam database...	0.85	0.81	0.89	17	1110	3	0	2	1	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.37	0.34	0.41	12	2016	18	1	16	1	23
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_X	-	0.75	0.57	1.00	4	540	0	0	0	0	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
3AKZ_H	tRNA links to Rfam database...	0.49	0.50	0.50	10	1107	12	3	7	2	10
3AM1_B	-	0.75	0.76	0.76	22	1437	7	3	4	0	7
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3IYQ_A	tmRNA links to Rfam database...	0.25	0.33	0.19	17	22350	86	39	34	13	34
3IZ4_A	tmRNA links to Rfam database...	0.59	0.56	0.63	53	25452	34	14	17	3	42
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	8	0	5	3	3
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_2	-	0.44	0.42	0.48	11	2227	19	0	12	7	15
3J0L_g	-	-0.01	0.00	0.00	0	173	5	1	2	2	2
3J0L_7	-	-0.01	0.00	0.00	0	516	3	1	2	0	10
3J16_L	tRNA links to Rfam database...	0.34	0.33	0.37	7	1140	12	0	12	0	14
3NDB_M	-	0.96	0.93	1.00	41	3673	4	0	0	4	3
3NKB_B	-	0.75	0.74	0.78	14	717	4	0	4	0	5
3NMU_E	-	1.00	1.00	1.00	3	213	4	0	0	4	0
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	7	0	2	5	8
3O58_2	5S_rRNA links to Rfam database...	0.87	0.90	0.85	28	2721	11	0	5	6	3
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	18	2	8	8	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...	0.82	0.80	0.85	40	4793	9	2	5	2	10
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...	0.78	0.72	0.84	21	1508	4	2	2	0	8
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
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	2	0	0	2	0
3TS0_U	-	1.00	1.00	1.00	6	112	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...	0.60	0.50	0.73	8	1282	7	3	0	4	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.81	0.86	30	2728	7	0	5	2	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	34	8	14	12	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10

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Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	1066
Total TN	115799
Total FP	610
Total FP CONTRA	148
Total FP INCONS	277
Total FP COMP	185
Total FN	311

Total Scores
MCC	0.741
Average MCC ± 95% Confidence Intervals	0.784 ± 0.070
Sensitivity	0.774
Positive Predictive Value	0.715
Nr of predictions	74

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.82	0.87	0.77	20	1998	15	6	0	9	3
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	0.87	0.88	0.88	7	141	1	0	1	0	1
2KZL_A	-	1.00	1.00	1.00	13	507	2	0	0	2	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...	1.00	1.00	1.00	23	740	0	0	0	0	0
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	-	0.85	0.86	0.86	6	268	3	0	1	2	1
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.89	0.86	0.93	25	2413	9	0	2	7	4
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	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...	0.64	0.73	0.57	8	1821	26	0	6	20	3
2XQD_Y	tRNA links to Rfam database...	1.00	1.00	1.00	21	1108	2	0	0	2	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.25	0.26	0.26	9	2011	26	1	24	1	26
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_X	-	0.53	0.57	0.50	4	536	7	1	3	3	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
3AKZ_H	tRNA links to Rfam database...	0.87	1.00	0.77	20	1101	9	6	0	3	0
3AM1_B	-	0.82	0.86	0.78	25	1434	7	3	4	0	4
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	9	0	5	4	4
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.18	17	22346	97	41	36	20	34
3IZ4_A	tmRNA links to Rfam database...	0.59	0.61	0.57	58	25435	49	17	26	6	37
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.91	0.89	32	2604	7	0	4	3	3
3J0L_h	-	0.89	0.88	0.90	28	2109	3	0	3	0	4
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_a	-	0.60	0.64	0.58	7	399	6	4	1	1	4
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_2	-	0.30	0.31	0.31	8	2224	27	1	17	9	18
3J0L_g	-	-0.02	0.00	0.00	0	171	7	1	4	2	2
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J16_L	tRNA links to Rfam database...	0.42	0.48	0.38	10	1133	16	3	13	0	11
3NDB_M	-	0.94	0.93	0.95	41	3671	8	0	2	6	3
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	-0.02	0.00	0.00	0	207	11	6	3	2	3
3NPB_A	SAM links to Rfam database...	0.79	0.73	0.87	27	2247	9	0	4	5	10
3O58_2	5S_rRNA links to Rfam database...	0.91	0.94	0.88	29	2721	10	0	4	6	2
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.29	11	4726	42	10	17	15	11
3OVB_D	-	1.00	1.00	1.00	11	215	2	0	0	2	0
3OVS_D	-	1.00	1.00	1.00	12	204	1	0	0	1	0
3P22_G	-	1.00	1.00	1.00	11	301	1	0	0	1	0
3PDR_A	ykoK links to Rfam database...	0.88	0.92	0.85	46	4786	10	5	3	2	4
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...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	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...	1.00	1.00	1.00	12	142	0	0	0	0	0
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3UZL_B	tRNA links to Rfam database...	0.92	1.00	0.84	16	1274	11	3	0	8	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7

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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 ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

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