CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(20)		MaxExpect
MCC	0.751	>	0.690
Average MCC ± 95% Confidence Intervals	0.754 ± 0.070	>	0.694 ± 0.083
Sensitivity	0.715	>	0.693
Positive Predictive Value	0.794	>	0.694
Total TP	615	>	596
Total TN	89177	>	89093
Total FP	319	<	419
Total FP CONTRA	63	<	71
Total FP INCONS	97	<	192
Total FP COMP	159	>	156
Total FN	245	<	264
P-value	5.23657817852e-08

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Performance plots

Comparison of performance of MXScarna(20) and MaxExpect. 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 MXScarna(20) and MaxExpect).
Comparison of performance of MXScarna(20) and MaxExpect. 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 MXScarna(20) and MaxExpect).
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 MXScarna(20) and MaxExpect).
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 MXScarna(20) and MaxExpect).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and MaxExpect. 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 MXScarna(20) and MaxExpect).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and MaxExpect. 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 MXScarna(20) and MaxExpect).

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

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

Total Base Pair Counts
Total TP	615
Total TN	89177
Total FP	319
Total FP CONTRA	63
Total FP INCONS	97
Total FP COMP	159
Total FN	245

Total Scores
MCC	0.751
Average MCC ± 95% Confidence Intervals	0.754 ± 0.070
Sensitivity	0.715
Positive Predictive Value	0.794
Nr of predictions	32

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2. Individual counts for MXScarna(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...	0.73	0.72	0.76	13	340	5	0	4	1	5
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	3	0	0	3	7
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.88	0.86	0.91	30	2012	4	0	3	1	5
3A2K_C	tRNA links to Rfam database...	0.74	0.73	0.76	16	1087	6	1	4	1	6
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	3	0	0	3	0
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	6	2	2	2	6
3IVN_B	Purine links to Rfam database...	0.81	0.74	0.89	17	884	2	2	0	0	6
3IZ4_A	tmRNA links to Rfam database...	0.58	0.54	0.63	51	25455	35	18	12	5	44
3IZF_C	5S_rRNA links to Rfam database...	0.87	0.89	0.86	31	2604	12	0	5	7	4
3J20_0	tRNA links to Rfam database...	0.93	0.90	0.95	19	1199	1	1	0	0	2
3J20_1	tRNA links to Rfam database...	0.97	0.95	1.00	19	1093	1	0	0	1	1
3J2L_3	5S_rRNA links to Rfam database...	0.67	0.65	0.71	22	2989	11	3	6	2	12
3JYV_7	tRNA links to Rfam database...	0.95	0.90	1.00	18	1093	2	0	0	2	2
3JYX_3	5S_rRNA links to Rfam database...	0.73	0.73	0.73	11	2363	26	0	4	22	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.70	0.83	0.59	10	4739	32	5	2	25	2
3LA5_A	Purine links to Rfam database...	0.87	0.80	0.95	20	933	1	1	0	0	5
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	9	2	4	3	10
3O58_3	5_8S_rRNA links to Rfam database...	0.62	0.59	0.65	13	4744	18	5	2	11	9
3O58_2	5S_rRNA links to Rfam database...	0.92	0.90	0.93	28	2724	13	0	2	11	3
3PDR_A	ykoK links to Rfam database...	0.85	0.82	0.89	41	4794	9	2	3	4	9
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	6	2	1	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.41	9	5352	15	3	10	2	20
3ZEX_D	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2763	13	0	4	9	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	36	8	11	17	15
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	12	0	6	6	8
4AOB_A	SAM links to Rfam database...	0.68	0.69	0.69	20	1408	13	2	7	4	9
4ENB_A	crcB links to Rfam database...	0.29	0.13	0.67	2	469	1	0	1	0	13
4ENC_A	crcB links to Rfam database...	0.68	0.47	1.00	7	489	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.65	0.58	0.74	14	1183	6	2	3	1	10

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Performance of MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP	596
Total TN	89093
Total FP	419
Total FP CONTRA	71
Total FP INCONS	192
Total FP COMP	156
Total FN	264

Total Scores
MCC	0.690
Average MCC ± 95% Confidence Intervals	0.694 ± 0.083
Sensitivity	0.693
Positive Predictive Value	0.694
Nr of predictions	32

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2. Individual counts for MaxExpect [ 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...	1.00	1.00	1.00	18	339	1	0	0	1	0
2WRQ_Y	tRNA links to Rfam database...	0.94	0.89	1.00	8	1144	14	0	0	14	1
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	26	0	6	20	3
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.24	0.26	0.25	9	2009	28	1	26	1	26
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	4
3GX2_A	SAM links to Rfam database...	0.93	0.89	0.96	25	1423	2	1	0	1	3
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.61	0.61	0.62	58	25442	42	14	22	6	37
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	8	0	5	3	3
3J20_0	tRNA links to Rfam database...	0.53	0.57	0.50	12	1195	13	2	10	1	9
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	6	0	5	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
3JYV_7	tRNA links to Rfam database...	0.48	0.45	0.53	9	1094	9	3	5	1	11
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	24	0	4	20	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.55	0.83	0.37	10	4729	34	14	3	17	2
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	10	0	6	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.40	0.50	0.33	11	4731	36	8	14	14	11
3O58_2	5S_rRNA links to Rfam database...	0.91	0.94	0.88	29	2721	11	0	4	7	2
3PDR_A	ykoK links to Rfam database...	0.92	0.90	0.94	45	4792	5	1	2	2	5
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.70	0.69	0.71	20	1505	8	3	5	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.54	0.45	0.65	13	5354	17	2	5	10	16
3ZEX_D	5S_rRNA links to Rfam database...	0.82	0.77	0.87	27	2765	11	0	4	7	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	10	17	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.81	0.86	30	2728	7	0	5	2	7
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.29	0.25	0.35	6	1185	11	4	7	0	18

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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 MXScarna(20) - scored higher in this pairwise comparison

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

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

Performance of MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

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