CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		Pknots
MCC	0.562	>	0.510
Average MCC ± 95% Confidence Intervals	0.518 ± 0.075	>	0.515 ± 0.077
Sensitivity	0.499	>	0.457
Positive Predictive Value	0.639	>	0.577
Total TP	927	>	848
Total TN	267554	>	267536
Total FP	612	<	692
Total FP CONTRA	67	=	67
Total FP INCONS	457	<	554
Total FP COMP	88	>	71
Total FN	930	<	1009
P-value	3.56938820447e-08

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Performance plots

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

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	927
Total TN	267554
Total FP	612
Total FP CONTRA	67
Total FP INCONS	457
Total FP COMP	88
Total FN	930

Total Scores
MCC	0.562
Average MCC ± 95% Confidence Intervals	0.518 ± 0.075
Sensitivity	0.499
Positive Predictive Value	0.639
Nr of predictions	54

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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	-	0.69	0.60	0.80	24	5121	11	2	4	5	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.45	0.32	0.67	6	621	3	0	3	0	13
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LKR_A	-	0.85	0.77	0.94	30	6073	4	0	2	2	9
2M58_A	-	-0.01	0.00	0.00	0	1638	15	0	15	0	17
2XQD_Y	tRNA links to Rfam database...	0.90	0.81	1.00	22	2828	1	0	0	1	5
3AKZ_H	tRNA links to Rfam database...	0.73	0.75	0.72	21	2672	8	4	4	0	7
3AM1_B	-	0.74	0.71	0.78	25	3208	7	1	6	0	10
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3IZF_C	5S_rRNA links to Rfam database...	0.72	0.61	0.85	33	6864	6	0	6	0	21
3J0L_a	-	0.55	0.50	0.62	8	1115	5	2	3	0	8
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_2	-	0.27	0.27	0.28	9	6184	26	2	21	3	24
3J0L_g	-	-0.01	0.00	0.00	0	458	7	2	5	0	4
3J16_L	tRNA links to Rfam database...	0.35	0.33	0.38	10	2749	16	1	15	0	20
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J20_1	tRNA links to Rfam database...	0.71	0.70	0.73	16	2904	7	0	6	1	7
3J2L_3	5S_rRNA links to Rfam database...	0.60	0.49	0.74	26	7840	11	0	9	2	27
3J3D_C	tRNA links to Rfam database...	0.46	0.43	0.50	12	2751	12	1	11	0	16
3J3E_7	5S_rRNA links to Rfam database...	0.47	0.35	0.63	19	7110	11	0	11	0	35
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7476	37	3	24	10	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.36	12	12213	35	3	18	14	24
3J3F_7	5S_rRNA links to Rfam database...	0.76	0.64	0.91	32	7225	3	0	3	0	18
3J3V_B	5S_rRNA links to Rfam database...	0.53	0.42	0.67	24	6985	12	1	11	0	33
3NDB_M	-	0.77	0.69	0.88	42	9132	7	0	6	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NPB_A	SAM links to Rfam database...	0.72	0.61	0.85	28	6988	8	1	4	3	18
3O58_3	5_8S_rRNA links to Rfam database...	0.31	0.34	0.29	12	12362	41	4	25	12	23
3O58_2	5S_rRNA links to Rfam database...	0.76	0.76	0.76	29	7222	10	3	6	1	9
3PDR_A	ykoK links to Rfam database...	0.74	0.64	0.85	46	12826	10	1	7	2	26
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.55	0.48	0.65	20	3885	11	2	9	0	22
3U4M_B	-	0.45	0.35	0.59	13	3138	9	1	8	0	24
3UZL_B	tRNA links to Rfam database...	0.73	0.62	0.85	23	3543	4	0	4	0	14
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.89	0.80	1.00	32	4721	1	0	0	1	8
3ZEX_G	-	0.77	0.66	0.91	49	16417	10	0	5	5	25
3ZEX_F	-	0.00	0.00	0.00	0	2620	11	2	6	3	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.31	0.47	16	14162	21	2	16	3	36
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.67	0.89	33	6984	4	0	4	0	16
3ZEX_H	-	0.19	0.18	0.19	7	9009	29	4	25	0	31
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	24	1	20	3	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.73	0.61	0.87	33	7102	6	1	4	1	21
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.32	0.30	0.38	3	520	5	1	4	0	7
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.45	0.42	0.50	8	1310	8	1	7	0	11
4FNJ_A	-	0.66	0.50	0.89	8	586	1	0	1	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.37	0.31	0.45	10	3464	12	3	9	0	22
4FRN_A	AdoCbl-variant links to Rfam database...	0.44	0.36	0.54	13	5127	11	2	9	0	23
4JF2_A	preQ1-II links to Rfam database...	0.80	0.71	0.92	22	2826	2	2	0	0	9
4JRC_A	-	0.25	0.22	0.31	5	1524	11	0	11	0	18

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Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	848
Total TN	267536
Total FP	692
Total FP CONTRA	67
Total FP INCONS	554
Total FP COMP	71
Total FN	1009

Total Scores
MCC	0.510
Average MCC ± 95% Confidence Intervals	0.515 ± 0.077
Sensitivity	0.457
Positive Predictive Value	0.577
Nr of predictions	54

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.67	0.58	0.79	23	5122	9	2	4	3	17
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.79	0.75	0.83	15	1522	3	1	2	0	5
2LKR_A	-	0.44	0.44	0.45	17	6067	22	4	17	1	22
2M58_A	-	0.51	0.41	0.64	7	1642	4	1	3	0	10
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3AKZ_H	tRNA links to Rfam database...	0.84	0.75	0.95	21	2679	1	1	0	0	7
3AM1_B	-	0.91	0.83	1.00	29	3211	0	0	0	0	6
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3J0L_a	-	0.35	0.31	0.42	5	1116	7	1	6	0	11
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J0L_2	-	0.36	0.36	0.36	12	6183	23	3	18	2	21
3J0L_g	-	-0.01	0.00	0.00	0	460	5	2	3	0	4
3J16_L	tRNA links to Rfam database...	0.34	0.30	0.41	9	2753	13	0	13	0	21
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.51	0.75	27	7839	12	0	9	3	26
3J3D_C	tRNA links to Rfam database...	0.46	0.43	0.50	12	2751	12	1	11	0	16
3J3E_7	5S_rRNA links to Rfam database...	0.43	0.35	0.54	19	7105	16	1	15	0	35
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.06	0.08	2	7479	33	2	20	11	31
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.36	0.37	13	12211	34	2	20	12	23
3J3F_7	5S_rRNA links to Rfam database...	0.27	0.24	0.32	12	7222	27	1	25	1	38
3J3V_B	5S_rRNA links to Rfam database...	0.41	0.33	0.51	19	6984	18	1	17	0	38
3NDB_M	-	0.77	0.69	0.88	42	9132	7	1	5	1	19
3NKB_B	-	0.55	0.50	0.62	13	1995	8	0	8	0	13
3NPB_A	SAM links to Rfam database...	0.76	0.67	0.86	31	6985	8	1	4	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.27	0.31	0.24	11	12357	38	11	24	3	24
3O58_2	5S_rRNA links to Rfam database...	0.83	0.74	0.93	28	7230	3	0	2	1	10
3PDR_A	ykoK links to Rfam database...	0.54	0.44	0.65	32	12831	19	0	17	2	40
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.65	0.52	0.81	22	3889	5	0	5	0	20
3U4M_B	-	0.26	0.22	0.32	8	3135	17	0	17	0	29
3UZL_B	tRNA links to Rfam database...	0.75	0.59	0.96	22	3547	1	0	1	0	15
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.71	0.63	0.81	25	4722	7	0	6	1	15
3ZEX_G	-	0.36	0.32	0.41	24	16413	37	3	31	3	50
3ZEX_F	-	0.00	0.00	0.00	0	2619	12	2	7	3	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.07	0.08	0.07	4	14141	54	4	47	3	48
3ZEX_D	5S_rRNA links to Rfam database...	0.27	0.24	0.30	12	6981	28	0	28	0	37
3ZEX_H	-	0.20	0.21	0.20	8	9005	32	5	27	0	30
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.25	8	11749	36	3	21	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4ATO_G	-	0.30	0.30	0.33	3	519	6	2	4	0	7
4ENB_A	crcB links to Rfam database...	0.83	0.79	0.88	15	1258	2	1	1	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FNJ_A	-	-0.02	0.00	0.00	0	585	10	0	10	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.48	0.38	0.63	12	3467	7	0	7	0	20
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.42	0.63	15	5127	9	1	8	0	21
4JF2_A	preQ1-II links to Rfam database...	0.81	0.77	0.86	24	2822	4	3	1	0	7
4JRC_A	-	0.81	0.70	0.94	16	1523	1	1	0	0	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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

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

Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

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