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)		CentroidAlifold(seed)
MCC	0.715	>	0.628
Average MCC ± 95% Confidence Intervals	0.699 ± 0.059	>	0.527 ± 0.081
Sensitivity	0.602	>	0.443
Positive Predictive Value	0.850	<	0.891
Total TP	935	>	688
Total TN	1251685	<	1252013
Total FP	203	>	99
Total FP CONTRA	18	>	9
Total FP INCONS	147	>	75
Total FP COMP	38	>	15
Total FN	617	<	864
P-value	5.19332990918e-08

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Performance plots

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

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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	935
Total TN	1251685
Total FP	203
Total FP CONTRA	18
Total FP INCONS	147
Total FP COMP	38
Total FN	617

Total Scores
MCC	0.715
Average MCC ± 95% Confidence Intervals	0.699 ± 0.059
Sensitivity	0.602
Positive Predictive Value	0.850
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...	0.40	0.30	0.55	6	1529	5	0	5	0	14
3J16_L	tRNA links to Rfam database...	0.82	0.70	0.95	21	2753	1	0	1	0	9
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	1	0	0	1	2
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.71	0.61	0.81	388	1116287	97	10	80	7	245
3J2L_3	5S_rRNA links to Rfam database...	0.77	0.62	0.94	33	7840	4	0	2	2	20
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	2	0	1	1	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.43	0.30	0.63	10	7487	8	0	6	2	23
3J3E_7	5S_rRNA links to Rfam database...	0.78	0.67	0.92	36	7101	3	0	3	0	18
3J3F_7	5S_rRNA links to Rfam database...	0.85	0.74	0.97	37	7222	2	0	1	1	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.63	0.53	0.76	19	12221	10	0	6	4	17
3J3V_B	5S_rRNA links to Rfam database...	0.76	0.61	0.95	35	6984	3	0	2	1	22
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	2	1	0	1	17
3W1K_J	tRNA-Sec links to Rfam database...	0.80	0.68	0.93	26	4158	3	1	1	1	12
3W3S_B	tRNA-Sec links to Rfam database...	0.78	0.65	0.93	26	4725	4	0	2	2	14
3ZEX_C	5_8S_rRNA links to Rfam database...	0.53	0.37	0.76	19	14171	10	1	5	4	33
3ZEX_D	5S_rRNA links to Rfam database...	0.82	0.73	0.92	36	6982	3	0	3	0	13
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...	0.83	0.70	0.97	38	7101	1	0	1	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.57	0.45	0.71	15	11760	12	0	6	6	18
4AOB_A	SAM links to Rfam database...	0.72	0.57	0.92	24	4345	3	0	2	1	18
4ENB_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1262	5	1	4	0	11
4ENC_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1313	5	1	4	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.74	0.63	0.87	20	3463	3	1	2	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	0.73	0.61	0.88	22	5126	3	2	1	0	14
4JF2_A	preQ1-II links to Rfam database...	0.72	0.52	1.00	16	2834	0	0	0	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	688
Total TN	1252013
Total FP	99
Total FP CONTRA	9
Total FP INCONS	75
Total FP COMP	15
Total FN	864

Total Scores
MCC	0.628
Average MCC ± 95% Confidence Intervals	0.527 ± 0.081
Sensitivity	0.443
Positive Predictive Value	0.891
Nr of predictions	26

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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
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	1540	0	0	0	0	20
3J16_L	tRNA links to Rfam database...	0.45	0.20	1.00	6	2769	0	0	0	0	24
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
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.72	0.60	0.86	381	1116321	70	5	58	7	252
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_7	5S_rRNA links to Rfam database...	0.58	0.34	1.00	17	7243	1	0	0	1	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.55	0.33	0.92	12	12233	1	0	1	0	24
3J3V_B	5S_rRNA links to Rfam database...	0.48	0.28	0.84	16	7002	3	0	3	0	41
3UZL_B	tRNA links to Rfam database...	0.40	0.16	1.00	6	3564	0	0	0	0	31
3W1K_J	tRNA-Sec links to Rfam database...	0.78	0.66	0.93	25	4159	2	1	1	0	13
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.60	0.92	24	4727	3	0	2	1	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.46	0.23	0.92	12	14183	1	1	0	0	40
3ZEX_D	5S_rRNA links to Rfam database...	0.60	0.37	1.00	18	7003	0	0	0	0	31
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.71	0.56	0.91	20	5129	2	1	1	0	16
4JF2_A	preQ1-II links to Rfam database...	0.72	0.52	1.00	16	2834	0	0	0	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 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 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 ]