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		HotKnots
MCC	0.633	>	0.549
Average MCC ± 95% Confidence Intervals	0.674 ± 0.091	>	0.636 ± 0.092
Sensitivity	0.523	>	0.485
Positive Predictive Value	0.769	>	0.626
Total TP	745	>	690
Total TN	280203	>	280069
Total FP	270	<	456
Total FP CONTRA	24	<	46
Total FP INCONS	200	<	367
Total FP COMP	46	>	43
Total FN	679	<	734
P-value	3.56938820447e-08

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Performance plots

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

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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	745
Total TN	280203
Total FP	270
Total FP CONTRA	24
Total FP INCONS	200
Total FP COMP	46
Total FN	679

Total Scores
MCC	0.633
Average MCC ± 95% Confidence Intervals	0.674 ± 0.091
Sensitivity	0.523
Positive Predictive Value	0.769
Nr of predictions	47

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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_a	-	0.71	0.56	0.90	9	1118	1	0	1	0	7
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_h	-	0.82	0.67	1.00	29	6076	2	0	0	2	14
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_1	-	0.70	0.58	0.85	11	1212	3	0	2	1	8
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
3J2C_M	-	0.72	0.57	0.92	118	106363	13	2	8	3	89
3J2C_O	-	0.83	0.70	1.00	44	10252	1	0	0	1	19
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_E	-	0.08	0.06	0.10	5	21896	44	5	39	0	72
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 HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	690
Total TN	280069
Total FP	456
Total FP CONTRA	46
Total FP INCONS	367
Total FP COMP	43
Total FN	734

Total Scores
MCC	0.549
Average MCC ± 95% Confidence Intervals	0.636 ± 0.092
Sensitivity	0.485
Positive Predictive Value	0.626
Nr of predictions	47

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2. Individual counts for HotKnots [ 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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
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	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
3J0L_a	-	0.51	0.50	0.53	8	1113	7	3	4	0	8
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J0L_h	-	0.75	0.60	0.93	26	6077	4	0	2	2	17
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_2	-	0.28	0.27	0.29	9	6185	23	3	19	1	24
3J16_L	tRNA links to Rfam database...	0.26	0.23	0.30	7	2752	16	1	15	0	23
3J20_1	tRNA links to Rfam database...	0.73	0.70	0.76	16	2905	7	0	5	2	7
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2C_M	-	0.61	0.49	0.76	102	106356	38	5	28	5	105
3J2C_O	-	0.60	0.49	0.74	31	10254	12	0	11	1	32
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
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	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.48	0.38	0.61	14	3547	9	0	9	0	23
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.50	0.61	20	4720	14	1	12	1	20
3ZEX_F	-	0.00	0.00	0.00	0	2617	11	2	9	0	12
3ZEX_G	-	0.66	0.57	0.76	42	16416	18	0	13	5	32
3ZEX_E	-	0.00	0.00	0.00	0	21893	54	4	48	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.78	0.67	0.92	33	6985	3	0	3	0	16
3ZEX_H	-	0.18	0.18	0.19	7	9008	30	5	25	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	14150	46	6	40	0	52
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	42	6	25	11	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.61	0.70	0.54	7	515	6	2	4	0	3
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.28	0.38	9	3462	15	0	15	0	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.52	0.44	0.62	16	5125	10	2	8	0	20
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 HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

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