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)		Pknots
MCC	0.867	>	0.550
Average MCC ± 95% Confidence Intervals	0.836 ± 0.062	>	0.585 ± 0.128
Sensitivity	0.826	>	0.587
Positive Predictive Value	0.913	>	0.525
Total TP	502	>	357
Total TN	51427	>	51297
Total FP	151	<	412
Total FP CONTRA	17	<	85
Total FP INCONS	31	<	238
Total FP COMP	103	>	89
Total FN	106	<	251
P-value	4.94031556815e-08

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Performance plots

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

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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	502
Total TN	51427
Total FP	151
Total FP CONTRA	17
Total FP INCONS	31
Total FP COMP	103
Total FN	106

Total Scores
MCC	0.867
Average MCC ± 95% Confidence Intervals	0.836 ± 0.062
Sensitivity	0.826
Positive Predictive Value	0.913
Nr of predictions	25

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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_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_7	5S_rRNA links to Rfam database...	0.99	0.97	1.00	35	2899	4	0	0	4	1
3J3F_8	5_8S_rRNA links to Rfam database...	0.86	0.84	0.89	16	4743	13	2	0	11	3
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_2	5_8S_rRNA links to Rfam database...	0.79	0.75	0.83	15	4498	12	1	2	9	5
4A1C_3	5S_rRNA links to Rfam database...	1.00	1.00	1.00	37	2726	2	0	0	2	0
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 Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	357
Total TN	51297
Total FP	412
Total FP CONTRA	85
Total FP INCONS	238
Total FP COMP	89
Total FN	251

Total Scores
MCC	0.550
Average MCC ± 95% Confidence Intervals	0.585 ± 0.128
Sensitivity	0.587
Positive Predictive Value	0.525
Nr of predictions	25

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2. Individual counts for Pknots [ 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...	0.83	0.83	0.83	15	510	3	2	1	0	3
3J16_L	tRNA links to Rfam database...	0.41	0.43	0.41	9	1137	13	1	12	0	12
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
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...	0.79	0.79	0.79	27	2986	12	1	6	5	7
3J3D_C	tRNA links to Rfam database...	0.46	0.53	0.42	10	944	14	5	9	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2720	33	5	15	13	13
3J3E_7	5S_rRNA links to Rfam database...	0.56	0.56	0.58	19	2708	16	2	12	2	15
3J3F_7	5S_rRNA links to Rfam database...	0.32	0.33	0.32	12	2896	27	2	24	1	24
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.53	0.33	10	4731	37	10	10	17	9
3J3V_B	5S_rRNA links to Rfam database...	0.58	0.63	0.55	17	2625	20	3	11	6	10
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	7	0	0	7	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...	0.78	0.76	0.81	25	1958	7	1	5	1	8
3ZEX_D	5S_rRNA links to Rfam database...	0.31	0.34	0.30	12	2756	28	5	23	0	23
3ZEX_C	5_8S_rRNA links to Rfam database...	0.10	0.14	0.08	4	5322	54	13	35	6	25
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	25	9	7	9	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2723	30	4	25	1	26
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.50	0.63	12	1183	7	0	7	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	0.57	0.54	0.63	15	1824	9	3	6	0	13
4JF2_A	preQ1-II links to Rfam database...	0.92	1.00	0.86	24	1054	4	4	0	0	0

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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 Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

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