CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidAlifold(20)		CentroidAlifold(seed)
MCC	0.673	>	0.589
Average MCC ± 95% Confidence Intervals	0.657 ± 0.063	>	0.560 ± 0.053
Sensitivity	0.516	>	0.379
Positive Predictive Value	0.879	<	0.920
Total TP	784	>	575
Total TN	286729	<	286996
Total FP	154	>	82
Total FP CONTRA	16	>	6
Total FP INCONS	92	>	44
Total FP COMP	46	>	32
Total FN	734	<	943
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	784
Total TN	286729
Total FP	154
Total FP CONTRA	16
Total FP INCONS	92
Total FP COMP	46
Total FN	734

Total Scores
MCC	0.673
Average MCC ± 95% Confidence Intervals	0.657 ± 0.063
Sensitivity	0.516
Positive Predictive Value	0.879
Nr of predictions	39

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.61	0.55	0.69	11	974	5	0	5	0	9
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...	0.46	0.25	0.83	5	4554	6	0	1	5	15
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...	0.44	0.19	1.00	8	5143	3	0	0	3	34
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...	0.78	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	3	4	0	81
3IZF_C	5S_rRNA links to Rfam database...	0.75	0.61	0.92	33	6867	4	0	3	1	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...	0.76	0.58	1.00	31	7844	2	0	0	2	22
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	7499	4	0	4	0	33
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	10	0	10	0	24
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.25	0.60	9	12231	6	1	5	0	27
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.68	0.92	34	7223	4	0	3	1	16
3J3V_B	5S_rRNA links to Rfam database...	0.66	0.47	0.93	27	6992	2	0	2	0	30
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_3	5S_rRNA links to Rfam database...	0.61	0.56	0.68	15	6306	20	0	7	13	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	9	12230	9	0	7	2	24
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...	0.70	0.54	0.89	25	6993	5	1	2	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.31	0.92	11	12391	1	0	1	0	24
3O58_2	5S_rRNA links to Rfam database...	0.78	0.76	0.81	29	7224	9	2	5	2	9
3PDR_A	ykoK links to Rfam database...	0.76	0.63	0.94	45	12832	5	0	3	2	27
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
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...	0.80	0.69	0.92	34	6984	3	0	3	0	15
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.21	0.69	11	14180	5	1	4	0	41
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	12	0	9	3	13
4A1C_3	5S_rRNA links to Rfam database...	0.76	0.63	0.92	34	7103	4	0	3	1	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.15	0.45	5	11770	8	1	5	2	28
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...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12
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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Performance of CentroidAlifold(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	575
Total TN	286996
Total FP	82
Total FP CONTRA	6
Total FP INCONS	44
Total FP COMP	32
Total FN	943

Total Scores
MCC	0.589
Average MCC ± 95% Confidence Intervals	0.560 ± 0.053
Sensitivity	0.379
Positive Predictive Value	0.920
Nr of predictions	39

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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
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...	0.24	0.12	0.50	2	2846	4	0	2	2	15
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.53	0.50	0.56	10	4542	20	0	8	12	10
2XQD_Y	tRNA links to Rfam database...	0.47	0.22	1.00	6	2844	0	0	0	0	21
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.77	0.64	0.93	27	5122	3	0	2	1	15
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_0	tRNA links to Rfam database...	0.45	0.20	1.00	6	2844	0	0	0	0	24
3J20_1	tRNA links to Rfam database...	0.51	0.26	1.00	6	2920	0	0	0	0	17
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 CentroidAlifold(20) - scored higher in this pairwise comparison

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

2. Individual counts for CentroidAlifold(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 ]