CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNASampler(20)		PknotsRG
MCC	0.612	>	0.557
Average MCC ± 95% Confidence Intervals	0.633 ± 0.067	>	0.573 ± 0.080
Sensitivity	0.471	<	0.494
Positive Predictive Value	0.799	>	0.633
Total TP	708	<	743
Total TN	283821	>	283534
Total FP	252	<	531
Total FP CONTRA	28	<	53
Total FP INCONS	150	<	377
Total FP COMP	74	<	101
Total FN	796	>	761
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNASampler(20) and PknotsRG. 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 RNASampler(20) and PknotsRG).
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 RNASampler(20) and PknotsRG).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(20) and PknotsRG. 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 RNASampler(20) and PknotsRG).

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Performance of RNASampler(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RNASampler(20)

Total Base Pair Counts
Total TP	708
Total TN	283821
Total FP	252
Total FP CONTRA	28
Total FP INCONS	150
Total FP COMP	74
Total FN	796

Total Scores
MCC	0.612
Average MCC ± 95% Confidence Intervals	0.633 ± 0.067
Sensitivity	0.471
Positive Predictive Value	0.799
Nr of predictions	38

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2. Individual counts for RNASampler(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3G4S_9	5S_rRNA links to Rfam database...	0.50	0.28	0.89	16	7363	2	1	1	0	41
3GX2_A	SAM links to Rfam database...	0.74	0.55	1.00	22	4349	1	0	0	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.47	0.32	0.69	42	70815	23	6	13	4	90
3IZF_C	5S_rRNA links to Rfam database...	0.74	0.57	0.97	31	6871	1	0	1	0	23
3J20_0	tRNA links to Rfam database...	0.80	0.67	0.95	20	2829	2	0	1	1	10
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...	0.45	0.32	0.63	17	7848	12	1	9	2	36
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_7	5S_rRNA links to Rfam database...	0.62	0.48	0.81	26	7108	6	0	6	0	28
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.09	0.18	3	7486	21	2	12	7	30
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.52	0.84	26	7229	5	0	5	0	24
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.33	0.46	12	12220	17	1	13	3	24
3J3V_B	5S_rRNA links to Rfam database...	0.63	0.42	0.96	24	6996	1	0	1	0	33
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.34	10	12217	26	4	15	7	23
3JYX_3	5S_rRNA links to Rfam database...	0.58	0.44	0.75	12	6312	11	0	4	7	15
3LA5_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2465	0	0	0	0	14
3NPB_A	SAM links to Rfam database...	0.68	0.48	0.96	22	6998	4	1	0	3	24
3O58_2	5S_rRNA links to Rfam database...	0.79	0.71	0.87	27	7229	5	2	2	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	18	2	8	8	23
3PDR_A	ykoK links to Rfam database...	0.70	0.53	0.93	38	12839	5	0	3	2	34
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...	0.67	0.48	0.95	20	3895	1	0	1	0	22
3ZEX_D	5S_rRNA links to Rfam database...	0.68	0.49	0.96	24	6996	1	0	1	0	25
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.19	0.38	10	14170	20	1	15	4	42
3ZND_W	tRNA links to Rfam database...	0.41	0.39	0.43	9	2982	15	2	10	3	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.23	5	11759	30	0	17	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.56	1.00	30	7110	0	0	0	0	24
4AOB_A	SAM links to Rfam database...	0.58	0.40	0.85	17	4351	4	0	3	1	25
4ENB_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1268	0	0	0	0	12
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.41	0.76	13	3469	4	0	4	0	19

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Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	743
Total TN	283534
Total FP	531
Total FP CONTRA	53
Total FP INCONS	377
Total FP COMP	101
Total FN	761

Total Scores
MCC	0.557
Average MCC ± 95% Confidence Intervals	0.573 ± 0.080
Sensitivity	0.494
Positive Predictive Value	0.633
Nr of predictions	38

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	13	5	3	5	8
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.54	0.42	0.71	24	7347	10	1	9	0	33
3GX2_A	SAM links to Rfam database...	0.67	0.55	0.81	22	4344	6	0	5	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.55	62	70763	52	10	41	1	70
3IZF_C	5S_rRNA links to Rfam database...	0.59	0.52	0.67	28	6861	14	1	13	0	26
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
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	0.53	0.74	28	7837	12	0	10	2	25
3J3D_C	tRNA links to Rfam database...	0.60	0.54	0.68	15	2753	7	0	7	0	13
3J3E_7	5S_rRNA links to Rfam database...	0.58	0.48	0.70	26	7103	11	1	10	0	28
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	7477	30	2	19	9	28
3J3F_7	5S_rRNA links to Rfam database...	0.80	0.70	0.92	35	7222	4	0	3	1	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.31	0.31	0.31	11	12211	37	4	20	13	25
3J3V_B	5S_rRNA links to Rfam database...	0.55	0.44	0.69	25	6985	11	1	10	0	32
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	1	21	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.32	10	12215	33	5	16	12	23
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	22	1	10	11	10
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.83	0.72	0.97	33	6987	3	0	1	2	13
3O58_2	5S_rRNA links to Rfam database...	0.59	0.61	0.58	23	7220	19	4	13	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3PDR_A	ykoK links to Rfam database...	0.75	0.63	0.90	45	12830	7	1	4	2	27
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...	0.61	0.50	0.75	21	3888	7	1	6	0	21
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.65	0.91	32	6986	3	0	3	0	17
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.21	0.28	11	14157	43	1	27	15	41
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	22	1	20	1	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.28	0.38	9	3462	15	0	15	0	23

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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 RNASampler(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RNASampler(20)

2. Individual counts for RNASampler(20) [ download as .csv ]

Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

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