CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	IPknot		McQFold
MCC	0.672	>	0.491
Average MCC ± 95% Confidence Intervals	0.743 ± 0.083	>	0.653 ± 0.093
Sensitivity	0.642	>	0.503
Positive Predictive Value	0.705	>	0.481
Total TP	1154	>	904
Total TN	953920	>	953676
Total FP	688	<	1132
Total FP CONTRA	125	<	252
Total FP INCONS	358	<	725
Total FP COMP	205	>	155
Total FN	643	<	893
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of IPknot and McQFold. 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 IPknot and McQFold).
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 IPknot and McQFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and McQFold. 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 IPknot and McQFold).

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Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	1154
Total TN	953920
Total FP	688
Total FP CONTRA	125
Total FP INCONS	358
Total FP COMP	205
Total FN	643

Total Scores
MCC	0.672
Average MCC ± 95% Confidence Intervals	0.743 ± 0.083
Sensitivity	0.642
Positive Predictive Value	0.705
Nr of predictions	56

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.33	0.55	6	517	5	1	4	0	12
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	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	-	0.88	0.86	0.89	25	2412	9	0	3	6	4
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
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2YIE_X	-	1.00	1.00	1.00	7	537	3	0	0	3	0
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3J0L_h	-	0.90	0.81	1.00	26	2114	2	0	0	2	6
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.16	0.18	0.18	2	400	10	3	6	1	9
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_7	-	-0.02	0.00	0.00	0	512	7	1	6	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_2	-	0.49	0.46	0.52	12	2227	18	0	11	7	14
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...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.75	0.74	0.76	305	421966	159	17	80	62	107
3J2C_M	-	0.72	0.74	0.71	71	39825	58	13	16	29	25
3J2C_O	-	0.98	0.95	1.00	39	3948	4	0	0	4	2
3J2L_3	5S_rRNA links to Rfam database...	0.82	0.82	0.82	28	2986	10	0	6	4	6
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.74	0.69	0.80	20	1508	5	0	5	0	9
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
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	-	0.91	0.91	0.91	20	1254	3	2	0	1	2
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...	0.94	0.91	0.97	30	1958	2	0	1	1	3
3ZEX_F	-	0.00	0.00	0.00	0	910	9	0	4	5	4
3ZEX_G	-	0.89	0.91	0.87	41	6460	18	5	1	12	4
3ZEX_E	-	0.00	0.00	0.00	0	8256	53	19	29	5	34
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.80	0.82	28	2762	10	0	6	4	7
3ZEX_B	-	0.33	0.27	0.40	95	421115	160	26	116	18	251
3ZEX_H	-	0.28	0.37	0.22	7	3593	25	15	10	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.51	0.34	0.77	10	5361	7	1	2	4	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	8	15
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.81	0.86	30	2728	7	0	5	2	7
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	0.49	0.57	0.44	4	211	6	0	5	1	3
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.59	0.53	0.67	8	484	4	0	4	0	7
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.79	0.71	0.87	20	1825	3	1	2	0	8
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	904
Total TN	953676
Total FP	1132
Total FP CONTRA	252
Total FP INCONS	725
Total FP COMP	155
Total FN	893

Total Scores
MCC	0.491
Average MCC ± 95% Confidence Intervals	0.653 ± 0.093
Sensitivity	0.503
Positive Predictive Value	0.481
Nr of predictions	56

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
2LDL_A	-	0.81	0.67	1.00	6	134	0	0	0	0	3
2LDT_A	-	0.79	0.64	1.00	7	155	0	0	0	0	4
2LHP_A	-	1.00	1.00	1.00	15	246	1	0	0	1	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	-	0.55	0.55	0.55	16	2411	15	5	8	2	13
2LQZ_A	-	1.00	1.00	1.00	8	124	3	0	0	3	0
2LWK_A	-	0.95	0.91	1.00	10	197	2	0	0	2	1
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
3AMU_B	tRNA links to Rfam database...	0.86	0.79	0.94	15	1141	4	0	1	3	4
3J0L_h	-	0.75	0.66	0.88	21	2116	3	0	3	0	11
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J0L_1	-	0.73	0.62	0.89	8	475	4	0	1	3	5
3J0L_7	-	-0.02	0.00	0.00	0	509	10	2	8	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_2	-	0.29	0.31	0.30	8	2223	21	1	18	2	18
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...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.55	0.56	0.55	231	421948	234	41	148	45	181
3J2C_M	-	0.38	0.44	0.34	42	39801	95	33	49	13	54
3J2C_O	-	0.62	0.61	0.64	25	3948	17	3	11	3	16
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	1	4	0	5
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
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	2	0	0	2	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	-	0.95	0.91	1.00	20	1256	2	0	0	2	2
3UZL_B	tRNA links to Rfam database...	0.62	0.75	0.52	12	1270	17	8	3	6	4
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.49	0.45	0.54	15	1961	14	1	12	1	18
3ZEX_F	-	0.00	0.00	0.00	0	910	9	0	4	5	4
3ZEX_G	-	0.36	0.40	0.34	18	6454	40	11	24	5	27
3ZEX_E	-	0.00	0.00	0.00	0	8256	53	17	31	5	34
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.66	0.88	23	2770	6	1	2	3	12
3ZEX_B	-	0.12	0.14	0.12	47	420944	379	78	283	18	299
3ZEX_H	-	0.27	0.37	0.21	7	3591	30	14	13	3	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.34	0.32	10	5343	25	4	17	4	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	33	11	16	6	15
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2724	30	4	24	2	26
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	-0.03	0.00	0.00	0	215	5	0	5	0	7
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	-	-0.04	0.00	0.00	0	243	7	0	7	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.82	0.71	0.95	20	1827	1	1	0	0	8
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 IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

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

Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

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