CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(20)		RSpredict(20)
MCC	0.645	>	0.544
Average MCC ± 95% Confidence Intervals	0.638 ± 0.060	>	0.531 ± 0.081
Sensitivity	0.499	>	0.425
Positive Predictive Value	0.838	>	0.701
Total TP	734	>	625
Total TN	280130	>	280115
Total FP	192	<	314
Total FP CONTRA	24	<	52
Total FP INCONS	118	<	214
Total FP COMP	50	>	48
Total FN	738	<	847
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAalifold(20) and RSpredict(20). 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 RNAalifold(20) and RSpredict(20)).
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 RNAalifold(20) and RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and RSpredict(20). 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 RNAalifold(20) and RSpredict(20)).

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

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

Total Base Pair Counts
Total TP	734
Total TN	280130
Total FP	192
Total FP CONTRA	24
Total FP INCONS	118
Total FP COMP	50
Total FN	738

Total Scores
MCC	0.645
Average MCC ± 95% Confidence Intervals	0.638 ± 0.060
Sensitivity	0.499
Positive Predictive Value	0.838
Nr of predictions	39

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2. Individual counts for RNAalifold(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...	0.60	0.36	1.00	4	402	0	0	0	0	7
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	3	0	0	3	16
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	7	5144	0	0	0	0	35
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...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3GX2_A	SAM links to Rfam database...	0.77	0.60	1.00	24	4347	1	0	0	1	16
3IVN_B	Purine links to Rfam database...	0.74	0.58	0.95	18	2327	1	1	0	0	13
3IZ4_A	tmRNA links to Rfam database...	0.53	0.35	0.82	46	70820	15	4	6	5	86
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.59	0.86	32	6866	5	1	4	0	22
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	0	0	0	0	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...	0.69	0.47	1.00	25	7850	2	0	0	2	28
3J3D_C	tRNA links to Rfam database...	0.80	0.68	0.95	19	2755	1	0	1	0	9
3J3E_7	5S_rRNA links to Rfam database...	0.69	0.56	0.86	30	7105	5	1	4	0	24
3J3E_8	5_8S_rRNA links to Rfam database...	0.23	0.15	0.36	5	7489	9	1	8	0	28
3J3F_7	5S_rRNA links to Rfam database...	0.74	0.58	0.94	29	7229	2	0	2	0	21
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.39	0.58	14	12222	17	1	9	7	22
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...	0.39	0.30	0.50	10	12226	15	0	10	5	23
3JYX_3	5S_rRNA links to Rfam database...	0.60	0.52	0.70	14	6308	17	0	6	11	13
3LA5_A	Purine links to Rfam database...	0.75	0.56	1.00	19	2466	0	0	0	0	15
3NPB_A	SAM links to Rfam database...	0.68	0.48	0.96	22	6998	3	1	0	2	24
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.26	0.53	9	12386	8	2	6	0	26
3O58_2	5S_rRNA links to Rfam database...	0.79	0.76	0.83	29	7225	7	3	3	1	9
3PDR_A	ykoK links to Rfam database...	0.76	0.61	0.96	44	12834	3	0	2	1	28
3RKF_A	Purine links to Rfam database...	0.68	0.50	0.94	17	2193	1	0	1	0	17
3SD1_A	THF links to Rfam database...	0.70	0.60	0.83	25	3886	5	1	4	0	17
3ZEX_D	5S_rRNA links to Rfam database...	0.80	0.69	0.92	34	6984	3	0	3	0	15
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	14	14171	14	1	10	3	38
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	11	0	9	2	13
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.57	0.97	31	7108	1	0	1	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	23	2	19	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.53	1.00	17	3469	0	0	0	0	15

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Performance of RSpredict(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	625
Total TN	280115
Total FP	314
Total FP CONTRA	52
Total FP INCONS	214
Total FP COMP	48
Total FN	847

Total Scores
MCC	0.544
Average MCC ± 95% Confidence Intervals	0.531 ± 0.081
Sensitivity	0.425
Positive Predictive Value	0.701
Nr of predictions	39

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2. Individual counts for RSpredict(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...	0.85	0.73	1.00	8	398	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.55	0.50	0.63	10	974	6	0	6	0	10
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4556	4	0	4	0	20
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.46	0.21	1.00	9	5142	0	0	0	0	33
3A2K_C	tRNA links to Rfam database...	0.78	0.68	0.90	19	2905	2	0	2	0	9
3AMU_B	tRNA links to Rfam database...	0.61	0.41	0.92	11	2991	1	0	1	0	16
3GX2_A	SAM links to Rfam database...	0.33	0.15	0.75	6	4363	2	0	2	0	34
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	0	1	0	11
3IZ4_A	tmRNA links to Rfam database...	0.53	0.43	0.65	57	70788	35	8	23	4	75
3IZF_C	5S_rRNA links to Rfam database...	0.75	0.61	0.92	33	6867	3	1	2	0	21
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...	0.66	0.48	0.92	11	2914	1	0	1	0	12
3J2L_3	5S_rRNA links to Rfam database...	0.58	0.40	0.84	21	7850	5	0	4	1	32
3J3D_C	tRNA links to Rfam database...	0.76	0.64	0.90	18	2755	2	0	2	0	10
3J3E_7	5S_rRNA links to Rfam database...	0.63	0.50	0.79	27	7106	7	1	6	0	27
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7484	19	4	15	0	33
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.68	0.92	34	7223	3	0	3	0	16
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.33	0.46	12	12220	23	2	12	9	24
3JYV_7	tRNA links to Rfam database...	0.77	0.63	0.95	20	2829	1	0	1	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.28	0.27	0.30	9	12216	33	5	16	12	24
3JYX_3	5S_rRNA links to Rfam database...	0.61	0.56	0.68	15	6306	13	0	7	6	12
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...	0.00	0.00	0.00	0	7015	6	1	5	0	46
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.34	0.30	12	12363	28	12	16	0	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...	0.67	0.49	0.92	35	12842	5	0	3	2	37
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...	0.68	0.60	0.78	25	3884	7	1	6	0	17
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.65	0.89	32	6985	4	1	3	0	17
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.19	0.36	10	14168	18	2	16	0	42
3ZND_W	tRNA links to Rfam database...	0.34	0.22	0.56	5	2994	7	0	4	3	18
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.33	0.69	18	7114	8	0	8	0	36
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.18	0.20	6	11751	30	6	18	6	27
4AOB_A	SAM links to Rfam database...	0.28	0.14	0.55	6	4360	5	0	5	0	36
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.45	0.32	0.67	6	1317	3	0	3	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.17	0.09	0.33	3	3477	6	0	6	0	29

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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 RNAalifold(20) - scored higher in this pairwise comparison

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

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

Performance of RSpredict(20) - scored lower in this pairwise comparison

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

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