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		MaxExpect
MCC	0.675	>	0.583
Average MCC ± 95% Confidence Intervals	0.748 ± 0.082	>	0.681 ± 0.092
Sensitivity	0.645	>	0.600
Positive Predictive Value	0.707	>	0.569
Total TP	1168	>	1086
Total TN	954095	>	953837
Total FP	688	<	1060
Total FP CONTRA	125	<	219
Total FP INCONS	358	<	604
Total FP COMP	205	<	237
Total FN	643	<	725
P-value	3.56938820447e-08

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Performance plots

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

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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	1168
Total TN	954095
Total FP	688
Total FP CONTRA	125
Total FP INCONS	358
Total FP COMP	205
Total FN	643

Total Scores
MCC	0.675
Average MCC ± 95% Confidence Intervals	0.748 ± 0.082
Sensitivity	0.645
Positive Predictive Value	0.707
Nr of predictions	57

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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
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	-	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_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
3J0L_a	-	0.16	0.18	0.18	2	400	10	3	6	1	9
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_h	-	0.90	0.81	1.00	26	2114	2	0	0	2	6
3J0L_7	-	-0.02	0.00	0.00	0	512	7	1	6	0	10
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 MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP	1086
Total TN	953837
Total FP	1060
Total FP CONTRA	219
Total FP INCONS	604
Total FP COMP	237
Total FN	725

Total Scores
MCC	0.583
Average MCC ± 95% Confidence Intervals	0.681 ± 0.092
Sensitivity	0.600
Positive Predictive Value	0.569
Nr of predictions	57

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2. Individual counts for MaxExpect [ 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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	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
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	-	0.84	0.83	0.86	24	2412	11	0	4	7	5
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	4
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_2	-	0.30	0.31	0.31	8	2224	25	2	16	7	18
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
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_h	-	0.93	0.88	1.00	28	2112	2	0	0	2	4
3J0L_7	-	-0.02	0.00	0.00	0	507	12	3	9	0	10
3J16_L	tRNA links to Rfam database...	0.34	0.33	0.37	7	1140	12	0	12	0	14
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	6	0	5	1	5
3J20_0	tRNA links to Rfam database...	0.53	0.57	0.50	12	1195	13	2	10	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.60	0.63	0.58	258	421926	239	28	156	55	154
3J2C_M	-	0.48	0.54	0.43	52	39804	88	29	40	19	44
3J2C_O	-	0.74	0.71	0.78	29	3950	13	0	8	5	12
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	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...	0.70	0.69	0.71	20	1505	8	3	5	0	9
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	142	0	0	0	0	0
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	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	8	0	0	8	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.97	0.94	1.00	31	1958	1	0	0	1	2
3ZEX_F	-	-0.01	0.00	0.00	0	908	11	2	4	5	4
3ZEX_G	-	0.98	0.96	1.00	43	6464	17	0	0	17	2
3ZEX_E	-	-0.01	0.00	0.00	0	8252	54	21	31	2	34
3ZEX_D	5S_rRNA links to Rfam database...	0.82	0.77	0.87	27	2765	11	0	4	7	8
3ZEX_B	-	0.37	0.39	0.35	134	420964	302	66	188	48	212
3ZEX_H	-	0.26	0.37	0.19	7	3589	29	18	11	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.54	0.45	0.65	13	5354	17	2	5	10	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	10	17	14	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...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.45	0.43	0.50	3	214	3	3	0	0	4
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...	0.36	0.33	0.42	5	484	8	0	7	1	10
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.29	0.25	0.35	6	1185	11	4	7	0	18
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.46	0.57	13	1825	10	5	5	0	15
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 MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

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