CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ContextFold		Pknots
MCC	0.642	>	0.491
Average MCC ± 95% Confidence Intervals	0.683 ± 0.093	>	0.594 ± 0.103
Sensitivity	0.537	>	0.445
Positive Predictive Value	0.773	>	0.549
Total TP	578	>	479
Total TN	141692	>	141568
Total FP	212	<	431
Total FP CONTRA	17	<	36
Total FP INCONS	153	<	357
Total FP COMP	42	>	38
Total FN	499	<	598
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of ContextFold 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 ContextFold 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 ContextFold and Pknots).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold 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 ContextFold and Pknots).

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	578
Total TN	141692
Total FP	212
Total FP CONTRA	17
Total FP INCONS	153
Total FP COMP	42
Total FN	499

Total Scores
MCC	0.642
Average MCC ± 95% Confidence Intervals	0.683 ± 0.093
Sensitivity	0.537
Positive Predictive Value	0.773
Nr of predictions	44

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2. Individual counts for ContextFold [ 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...	0.55	0.50	0.63	10	1524	6	0	6	0	10
2LDL_A	-	0.90	0.82	1.00	9	342	0	0	0	0	2
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	0.93	0.88	1.00	7	344	2	0	0	2	1
2LK3_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2LKR_A	-	0.65	0.56	0.76	22	6076	9	0	7	2	17
2LQZ_A	-	0.80	0.73	0.89	8	342	1	1	0	0	3
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
3J0L_h	-	0.82	0.67	1.00	29	6076	2	0	0	2	14
3J0L_a	-	0.71	0.56	0.90	9	1118	1	0	1	0	7
3J0L_1	-	0.70	0.58	0.85	11	1212	3	0	2	1	8
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_2	-	0.64	0.61	0.69	20	6187	11	2	7	2	13
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.62	1.00	33	7842	2	0	0	2	20
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	0	0	0	0	1
3TS0_U	-	1.00	1.00	1.00	6	247	0	0	0	0	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.75	0.57	1.00	21	3139	0	0	0	0	16
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.79	0.70	0.90	28	4722	4	0	3	1	12
3ZEX_F	-	0.00	0.00	0.00	0	2617	16	2	9	5	12
3ZEX_G	-	0.26	0.20	0.33	15	16426	34	2	28	4	59
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.67	0.97	33	6987	1	0	1	0	16
3ZEX_H	-	0.22	0.21	0.24	8	9011	26	2	24	0	30
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	13	14167	22	1	15	6	39
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ATO_G	-	-0.01	0.00	0.00	0	526	2	0	2	0	10
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...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.71	0.56	0.90	18	3466	2	1	1	0	14
4FRN_A	AdoCbl-variant links to Rfam database...	0.40	0.33	0.50	12	5127	12	3	9	0	24
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0

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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	479
Total TN	141568
Total FP	431
Total FP CONTRA	36
Total FP INCONS	357
Total FP COMP	38
Total FN	598

Total Scores
MCC	0.491
Average MCC ± 95% Confidence Intervals	0.594 ± 0.103
Sensitivity	0.445
Positive Predictive Value	0.549
Nr of predictions	44

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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...	0.79	0.75	0.83	15	1522	3	1	2	0	5
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.44	0.44	0.45	17	6067	22	4	17	1	22
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.33	0.23	0.50	3	490	3	0	3	0	10
3J0L_h	-	0.58	0.49	0.70	21	6075	11	0	9	2	22
3J0L_a	-	0.35	0.31	0.42	5	1116	7	1	6	0	11
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J0L_g	-	-0.01	0.00	0.00	0	460	5	2	3	0	4
3J0L_2	-	0.36	0.36	0.36	12	6183	23	3	18	2	21
3J16_L	tRNA links to Rfam database...	0.34	0.30	0.41	9	2753	13	0	13	0	21
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.51	0.75	27	7839	12	0	9	3	26
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.26	0.22	0.32	8	3135	17	0	17	0	29
3UZL_B	tRNA links to Rfam database...	0.75	0.59	0.96	22	3547	1	0	1	0	15
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.71	0.63	0.81	25	4722	7	0	6	1	15
3ZEX_F	-	0.00	0.00	0.00	0	2619	12	2	7	3	12
3ZEX_G	-	0.36	0.32	0.41	24	16413	37	3	31	3	50
3ZEX_D	5S_rRNA links to Rfam database...	0.27	0.24	0.30	12	6981	28	0	28	0	37
3ZEX_H	-	0.20	0.21	0.20	8	9005	32	5	27	0	30
3ZEX_C	5_8S_rRNA links to Rfam database...	0.07	0.08	0.07	4	14141	54	4	47	3	48
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.25	8	11749	36	3	21	12	25
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4ATO_G	-	0.30	0.30	0.33	3	519	6	2	4	0	7
4ENB_A	crcB links to Rfam database...	0.83	0.79	0.88	15	1258	2	1	1	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FNJ_A	-	-0.02	0.00	0.00	0	585	10	0	10	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.48	0.38	0.63	12	3467	7	0	7	0	20
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.42	0.63	15	5127	9	1	8	0	21
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	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 ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

2. Individual counts for ContextFold [ 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 ]