CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PETfold_pre2.0(seed)		MaxExpect
MCC	0.866	>	0.617
Average MCC ± 95% Confidence Intervals	0.837 ± 0.059	>	0.584 ± 0.118
Sensitivity	0.841	>	0.627
Positive Predictive Value	0.892	>	0.609
Total TP	858	>	640
Total TN	473383	>	473294
Total FP	280	<	567
Total FP CONTRA	35	<	94
Total FP INCONS	69	<	317
Total FP COMP	176	>	156
Total FN	162	<	380
P-value	5.06544643719e-08

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Performance plots

Comparison of performance of PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) and MaxExpect).
Comparison of performance of PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) and MaxExpect).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) and MaxExpect).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) and MaxExpect).

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Performance of PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

Total Base Pair Counts
Total TP	858
Total TN	473383
Total FP	280
Total FP CONTRA	35
Total FP INCONS	69
Total FP COMP	176
Total FN	162

Total Scores
MCC	0.866
Average MCC ± 95% Confidence Intervals	0.837 ± 0.059
Sensitivity	0.841
Positive Predictive Value	0.892
Nr of predictions	26

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2. Individual counts for PETfold_pre2.0(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.33	0.55	6	517	5	0	5	0	12
3J16_L	tRNA links to Rfam database...	1.00	1.00	1.00	21	1138	1	0	0	1	0
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	2	0	0	2	0
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.86	0.86	0.86	356	421956	129	18	38	73	56
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J2L_3	5S_rRNA links to Rfam database...	0.97	0.94	1.00	32	2988	5	0	0	5	2
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	4	3	0	1	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.71	0.67	0.77	10	2729	8	1	2	5	5
3J3E_7	5S_rRNA links to Rfam database...	0.97	0.97	0.97	33	2707	6	0	1	5	1
3J3F_8	5_8S_rRNA links to Rfam database...	0.86	0.84	0.89	16	4743	13	2	0	11	3
3J3F_7	5S_rRNA links to Rfam database...	0.99	0.97	1.00	35	2899	4	0	0	4	1
3J3V_B	5S_rRNA links to Rfam database...	0.90	0.89	0.92	24	2630	14	0	2	12	3
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	8	0	0	8	2
3W1K_J	tRNA-Sec links to Rfam database...	0.85	0.81	0.89	25	1650	4	2	1	1	6
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.73	0.89	24	1962	6	1	2	3	9
3ZEX_D	5S_rRNA links to Rfam database...	0.96	0.94	0.97	33	2762	6	0	1	5	2
3ZEX_C	5_8S_rRNA links to Rfam database...	0.70	0.59	0.85	17	5354	12	1	2	9	12
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	16	0	4	12	2
4A1C_3	5S_rRNA links to Rfam database...	1.00	1.00	1.00	37	2726	2	0	0	2	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.79	0.75	0.83	15	4498	12	1	2	9	5
4AOB_A	SAM links to Rfam database...	0.85	0.79	0.92	23	1412	4	0	2	2	6
4ENB_A	crcB links to Rfam database...	0.61	0.53	0.73	8	461	5	1	2	2	7
4ENC_A	crcB links to Rfam database...	0.61	0.53	0.73	8	485	5	1	2	2	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.87	0.83	0.91	20	1180	3	0	2	1	4
4FRN_A	AdoCbl-variant links to Rfam database...	0.83	0.79	0.88	22	1823	3	2	1	0	6
4JF2_A	preQ1-II links to Rfam database...	0.76	0.63	0.94	15	1066	1	1	0	0	9

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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	640
Total TN	473294
Total FP	567
Total FP CONTRA	94
Total FP INCONS	317
Total FP COMP	156
Total FN	380

Total Scores
MCC	0.617
Average MCC ± 95% Confidence Intervals	0.584 ± 0.118
Sensitivity	0.627
Positive Predictive Value	0.609
Nr of predictions	26

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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
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3J16_L	tRNA links to Rfam database...	0.34	0.33	0.37	7	1140	12	0	12	0	14
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	6	0	5	1	5
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.60	0.63	0.58	258	421926	239	28	156	55	154
3J20_0	tRNA links to Rfam database...	0.53	0.57	0.50	12	1195	13	2	10	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
3J3D_C	tRNA links to Rfam database...	0.47	0.53	0.43	10	945	13	5	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2719	32	5	16	11	13
3J3E_7	5S_rRNA links to Rfam database...	0.60	0.59	0.63	20	2709	14	2	10	2	14
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.42	0.29	8	4733	39	10	10	19	11
3J3F_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	34	2898	4	1	1	2	2
3J3V_B	5S_rRNA links to Rfam database...	0.71	0.74	0.69	20	2627	17	2	7	8	7
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	8	0	0	8	0
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.97	0.94	1.00	31	1958	1	0	0	1	2
3ZEX_D	5S_rRNA links to Rfam database...	0.82	0.77	0.87	27	2765	11	0	4	7	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.54	0.45	0.65	13	5354	17	2	5	10	16
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	25	9	7	9	5
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.81	0.86	30	2728	7	0	5	2	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	10	17	14	15
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.46	0.57	13	1825	10	5	5	0	15
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

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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 PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

2. Individual counts for PETfold_pre2.0(seed) [ 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 ]