CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Carnac(20)		CentroidAlifold(seed)
MCC	0.592	>	0.587
Average MCC ± 95% Confidence Intervals	0.563 ± 0.076	>	0.555 ± 0.056
Sensitivity	0.392	>	0.368
Positive Predictive Value	0.898	<	0.941
Total TP	563	>	528
Total TN	276293	<	276359
Total FP	90	>	52
Total FP CONTRA	8	>	6
Total FP INCONS	56	>	27
Total FP COMP	26	>	19
Total FN	873	<	908
P-value	0.014979478926

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Performance plots

Comparison of performance of Carnac(20) and CentroidAlifold(seed). 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 Carnac(20) and CentroidAlifold(seed)).
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 Carnac(20) and CentroidAlifold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Carnac(20) and CentroidAlifold(seed). 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 Carnac(20) and CentroidAlifold(seed)).

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

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

Total Base Pair Counts
Total TP	563
Total TN	276293
Total FP	90
Total FP CONTRA	8
Total FP INCONS	56
Total FP COMP	26
Total FN	873

Total Scores
MCC	0.592
Average MCC ± 95% Confidence Intervals	0.563 ± 0.076
Sensitivity	0.392
Positive Predictive Value	0.898
Nr of predictions	36

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	0.79	0.63	1.00	17	2833	0	0	0	0	10
3A2K_C	tRNA links to Rfam database...	0.78	0.61	1.00	17	2909	0	0	0	0	11
3AMU_B	tRNA links to Rfam database...	0.69	0.59	0.80	16	2983	6	0	4	2	11
3GX2_A	SAM links to Rfam database...	0.57	0.33	1.00	13	4358	0	0	0	0	27
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	0.23	0.94	31	70843	2	0	2	0	101
3IZF_C	5S_rRNA links to Rfam database...	0.73	0.56	0.97	30	6872	1	0	1	0	24
3J20_1	tRNA links to Rfam database...	0.86	0.74	1.00	17	2909	0	0	0	0	6
3J20_0	tRNA links to Rfam database...	0.62	0.53	0.73	16	2828	7	0	6	1	14
3J2L_3	5S_rRNA links to Rfam database...	0.46	0.34	0.64	18	7847	11	0	10	1	35
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
3J3E_7	5S_rRNA links to Rfam database...	0.65	0.44	0.96	24	7115	1	0	1	0	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	9	12237	0	0	0	0	27
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.44	1.00	22	7238	0	0	0	0	28
3J3V_B	5S_rRNA links to Rfam database...	0.58	0.35	0.95	20	7000	1	0	1	0	37
3JYV_7	tRNA links to Rfam database...	0.68	0.50	0.94	16	2833	1	0	1	0	16
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	15	6308	10	1	4	5	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	12239	2	0	0	2	26
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...	0.44	0.20	1.00	9	7012	2	0	0	2	37
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.26	1.00	9	12394	0	0	0	0	26
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3PDR_A	ykoK links to Rfam database...	0.62	0.40	0.97	29	12850	3	0	1	2	43
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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.53	1.00	26	6995	0	0	0	0	23
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.13	0.70	7	14186	3	1	2	0	45
3ZND_W	tRNA links to Rfam database...	0.47	0.39	0.56	9	2987	10	0	7	3	14
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
4AOB_A	SAM links to Rfam database...	0.49	0.33	0.74	14	4352	6	1	4	1	28
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19
4FRG_B	AdoCbl-variant links to Rfam database...	0.43	0.19	1.00	6	3480	0	0	0	0	26

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Performance of CentroidAlifold(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidAlifold(seed)

Total Base Pair Counts
Total TP	528
Total TN	276359
Total FP	52
Total FP CONTRA	6
Total FP INCONS	27
Total FP COMP	19
Total FN	908

Total Scores
MCC	0.587
Average MCC ± 95% Confidence Intervals	0.555 ± 0.056
Sensitivity	0.368
Positive Predictive Value	0.941
Nr of predictions	36

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2. Individual counts for CentroidAlifold(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2WRQ_Y	tRNA links to Rfam database...	0.24	0.12	0.50	2	2846	4	0	2	2	15
2XQD_Y	tRNA links to Rfam database...	0.47	0.22	1.00	6	2844	0	0	0	0	21
3A2K_C	tRNA links to Rfam database...	0.46	0.21	1.00	6	2920	0	0	0	0	22
3AMU_B	tRNA links to Rfam database...	0.47	0.22	1.00	6	2997	0	0	0	0	21
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...	0.78	0.65	0.95	20	2325	1	1	0	0	11
3IZ4_A	tmRNA links to Rfam database...	0.58	0.39	0.88	51	70818	7	2	5	0	81
3IZF_C	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	6887	0	0	0	0	38
3J20_1	tRNA links to Rfam database...	0.51	0.26	1.00	6	2920	0	0	0	0	17
3J20_0	tRNA links to Rfam database...	0.45	0.20	1.00	6	2844	0	0	0	0	24
3J2L_3	5S_rRNA links to Rfam database...	0.53	0.28	1.00	15	7860	2	0	0	2	38
3J3D_C	tRNA links to Rfam database...	0.46	0.21	1.00	6	2769	0	0	0	0	22
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.09	0.75	3	7499	1	0	1	0	30
3J3E_7	5S_rRNA links to Rfam database...	0.56	0.33	0.95	18	7121	1	0	1	0	36
3J3F_8	5_8S_rRNA links to Rfam database...	0.55	0.33	0.92	12	12233	1	0	1	0	24
3J3F_7	5S_rRNA links to Rfam database...	0.58	0.34	1.00	17	7243	1	0	0	1	33
3J3V_B	5S_rRNA links to Rfam database...	0.48	0.28	0.84	16	7002	3	0	3	0	41
3JYV_7	tRNA links to Rfam database...	0.43	0.19	1.00	6	2844	0	0	0	0	26
3JYX_3	5S_rRNA links to Rfam database...	0.59	0.41	0.85	11	6315	5	0	2	3	16
3JYX_4	5_8S_rRNA links to Rfam database...	0.52	0.30	0.91	10	12235	3	0	1	2	23
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...	0.71	0.54	0.93	25	6994	4	1	1	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.56	0.34	0.92	12	12390	1	0	1	0	23
3O58_2	5S_rRNA links to Rfam database...	0.65	0.42	1.00	16	7244	0	0	0	0	22
3PDR_A	ykoK links to Rfam database...	0.77	0.61	0.98	44	12835	3	0	1	2	28
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...	0.71	0.52	0.96	22	3893	1	0	1	0	20
3ZEX_D	5S_rRNA links to Rfam database...	0.60	0.37	1.00	18	7003	0	0	0	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.46	0.23	0.92	12	14183	1	1	0	0	40
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	2998	6	0	5	1	23
4A1C_3	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	7124	0	0	0	0	38
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.24	0.89	8	11772	3	0	1	2	25
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1267	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1318	0	0	0	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.69	0.53	0.89	17	3467	2	1	1	0	15

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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 Carnac(20) - scored higher in this pairwise comparison

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

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

Performance of CentroidAlifold(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidAlifold(seed)

2. Individual counts for CentroidAlifold(seed) [ download as .csv ]