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	0.760	>	0.661
Average MCC ± 95% Confidence Intervals	0.754 ± 0.097	>	0.707 ± 0.096
Sensitivity	0.742	>	0.689
Positive Predictive Value	0.784	>	0.640
Total TP	692	>	643
Total TN	105927	>	105805
Total FP	323	<	503
Total FP CONTRA	60	<	114
Total FP INCONS	131	<	248
Total FP COMP	132	<	141
Total FN	241	<	290
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	692
Total TN	105927
Total FP	323
Total FP CONTRA	60
Total FP INCONS	131
Total FP COMP	132
Total FN	241

Total Scores
MCC	0.760
Average MCC ± 95% Confidence Intervals	0.754 ± 0.097
Sensitivity	0.742
Positive Predictive Value	0.784
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...	0.58	0.56	0.63	10	512	6	0	6	0	8
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	0.92	0.86	1.00	6	124	3	0	0	3	1
2LK3_A	-	0.94	0.89	1.00	8	92	0	0	0	0	1
2LKR_A	-	0.70	0.66	0.76	19	2415	12	0	6	6	10
2LQZ_A	-	1.00	1.00	1.00	8	124	1	0	0	1	0
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
3J0L_a	-	0.80	0.73	0.89	8	402	2	0	1	1	3
3J0L_g	-	-0.01	0.00	0.00	0	174	3	0	2	1	2
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_h	-	0.95	0.91	1.00	29	2111	2	0	0	2	3
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.75	0.69	0.82	9	473	5	0	2	3	4
3J0L_2	-	0.80	0.77	0.83	20	2226	11	0	4	7	6
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
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
3J2C_M	-	0.97	0.97	0.98	93	39830	38	0	2	36	3
3J2C_O	-	1.00	1.00	1.00	41	3946	4	0	0	4	0
3J2L_3	5S_rRNA links to Rfam database...	0.95	0.91	1.00	31	2989	4	0	0	4	3
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	0	0	0	0	0
3TS0_U	-	1.00	1.00	1.00	6	112	0	0	0	0	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.98	0.95	1.00	21	1255	0	0	0	0	1
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.85	0.90	28	1958	4	0	3	1	5
3ZEX_F	-	0.00	0.00	0.00	0	910	16	0	4	12	4
3ZEX_G	-	0.32	0.31	0.33	14	6465	35	10	18	7	31
3ZEX_E	-	0.12	0.15	0.10	5	8255	44	20	24	0	29
3ZEX_D	5S_rRNA links to Rfam database...	0.92	0.86	1.00	30	2766	4	0	0	4	5
3ZEX_H	-	0.29	0.37	0.24	7	3596	27	7	15	5	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.41	0.48	12	5349	23	4	9	10	17
4A1C_3	5S_rRNA links to Rfam database...	0.96	0.92	1.00	34	2729	1	0	0	1	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ATO_G	-	-0.02	0.00	0.00	0	218	2	1	1	0	7
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.77	0.71	0.85	17	1182	3	2	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.42	0.39	0.46	11	1824	13	6	7	0	17
4HXH_A	-	1.00	1.00	1.00	6	89	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	643
Total TN	105805
Total FP	503
Total FP CONTRA	114
Total FP INCONS	248
Total FP COMP	141
Total FN	290

Total Scores
MCC	0.661
Average MCC ± 95% Confidence Intervals	0.707 ± 0.096
Sensitivity	0.689
Positive Predictive Value	0.640
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...	0.64	0.61	0.69	11	512	5	0	5	0	7
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	1.00	1.00	1.00	29	2411	8	0	0	8	0
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3J0L_g	-	-0.01	0.00	0.00	0	173	5	1	2	2	2
3J0L_7	-	0.38	0.50	0.31	5	503	12	4	7	1	5
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_2	-	0.34	0.35	0.35	9	2224	23	2	15	6	17
3J16_L	tRNA links to Rfam database...	0.31	0.33	0.30	7	1136	16	3	13	0	14
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	8	0	5	3	5
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J2C_M	-	0.83	0.85	0.81	82	39824	58	8	11	39	14
3J2C_O	-	0.71	0.68	0.74	28	3949	15	3	7	5	13
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.49	0.50	0.50	8	1277	15	0	8	7	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.61	0.61	20	1956	14	4	9	1	13
3ZEX_F	-	-0.01	0.00	0.00	0	908	11	2	4	5	4
3ZEX_G	-	0.86	0.84	0.88	38	6464	22	0	5	17	7
3ZEX_E	-	0.00	0.00	0.00	0	8255	54	17	32	5	34
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	6	0	2	4	5
3ZEX_H	-	0.26	0.37	0.19	7	3588	30	19	11	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	5328	46	11	35	0	29
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	12	16	14	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.72	1.00	0.54	7	207	6	6	0	0	0
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
4HXH_A	-	1.00	1.00	1.00	6	89	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 ]