CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	HotKnots		MCFold
MCC	0.545	>	0.385
Average MCC ± 95% Confidence Intervals	0.531 ± 0.067	>	0.375 ± 0.065
Sensitivity	0.486	>	0.396
Positive Predictive Value	0.617	>	0.383
Total TP	998	>	814
Total TN	287423	>	286913
Total FP	706	<	1445
Total FP CONTRA	80	<	176
Total FP INCONS	540	<	1138
Total FP COMP	86	<	131
Total FN	1056	<	1240
P-value	3.56938820447e-08

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Performance plots

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

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Performance of HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	998
Total TN	287423
Total FP	706
Total FP CONTRA	80
Total FP INCONS	540
Total FP COMP	86
Total FN	1056

Total Scores
MCC	0.545
Average MCC ± 95% Confidence Intervals	0.531 ± 0.067
Sensitivity	0.486
Positive Predictive Value	0.617
Nr of predictions	66

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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
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KFC_A	-	-0.02	0.00	0.00	0	623	7	0	7	0	20
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2M58_A	-	0.34	0.29	0.42	5	1641	7	1	6	0	12
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_E	-	0.53	0.29	1.00	4	557	0	0	0	0	10
2WW9_D	-	0.14	0.12	0.19	3	1937	13	0	13	0	23
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WWQ_V	tRNA links to Rfam database...	0.76	0.68	0.86	19	2904	5	0	3	2	9
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2ZZN_D	tRNA links to Rfam database...	0.82	0.78	0.88	21	2461	3	0	3	0	6
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3AKZ_H	tRNA links to Rfam database...	0.43	0.39	0.48	11	2678	12	2	10	0	17
3AM1_B	-	0.78	0.71	0.86	25	3211	4	0	4	0	10
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.68	0.55	0.85	22	4345	5	0	4	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.63	0.58	0.70	19	4251	9	0	8	1	14
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
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_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_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3J3D_C	tRNA links to Rfam database...	0.28	0.25	0.32	7	2753	15	1	14	0	21
3J3E_7	5S_rRNA links to Rfam database...	0.59	0.50	0.71	27	7102	11	1	10	0	27
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.09	0.11	3	7476	33	2	22	9	30
3J3F_7	5S_rRNA links to Rfam database...	0.73	0.64	0.84	32	7222	7	0	6	1	18
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.30	11	12209	40	3	23	14	25
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	1	21	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.33	10	12216	31	5	15	11	23
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	22	1	10	11	10
3KTW_C	-	0.73	0.63	0.84	27	4528	6	2	3	1	16
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.84	0.74	0.96	45	9133	3	0	2	1	16
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3O58_2	5S_rRNA links to Rfam database...	0.71	0.71	0.71	27	7222	12	4	7	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.23	0.26	0.21	9	12360	34	10	24	0	26
3PDR_A	ykoK links to Rfam database...	0.67	0.56	0.82	40	12831	11	0	9	2	32
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.64	0.52	0.79	22	3888	6	1	5	0	20
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3ZEX_H	-	0.18	0.18	0.19	7	9008	30	5	25	0	31
3ZEX_G	-	0.66	0.57	0.76	42	16416	18	0	13	5	32
3ZEX_D	5S_rRNA links to Rfam database...	0.78	0.67	0.92	33	6985	3	0	3	0	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	14150	46	6	40	0	52
3ZEX_F	-	0.00	0.00	0.00	0	2617	11	2	9	0	12
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	22	1	20	1	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	42	6	25	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
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
4JF2_A	preQ1-II links to Rfam database...	0.81	0.77	0.86	24	2822	4	3	1	0	7
4JRC_A	-	0.29	0.26	0.35	6	1523	11	0	11	0	17

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Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

Total Base Pair Counts
Total TP	814
Total TN	286913
Total FP	1445
Total FP CONTRA	176
Total FP INCONS	1138
Total FP COMP	131
Total FN	1240

Total Scores
MCC	0.385
Average MCC ± 95% Confidence Intervals	0.375 ± 0.065
Sensitivity	0.396
Positive Predictive Value	0.383
Nr of predictions	66

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	1	0	0	1	1
2KFC_A	-	0.28	0.25	0.36	5	616	9	2	7	0	15
2KX8_A	7SK links to Rfam database...	0.91	0.89	0.94	16	844	2	0	1	1	2
2LA5_A	-	-0.03	0.00	0.00	0	615	15	0	15	0	19
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.45	0.39	9	1517	16	0	14	2	11
2LKR_A	-	0.93	0.92	0.95	36	6067	14	0	2	12	3
2M58_A	-	0.20	0.24	0.18	4	1631	19	2	16	1	13
2RP0_A	-	0.44	0.42	0.50	5	341	5	1	4	0	7
2WRQ_Y	tRNA links to Rfam database...	0.27	0.35	0.22	6	2823	25	8	13	4	11
2WW9_E	-	-0.02	0.00	0.00	0	547	14	0	14	0	14
2WW9_D	-	-0.01	0.00	0.00	0	1925	28	5	23	0	26
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WWQ_V	tRNA links to Rfam database...	0.15	0.18	0.15	5	2892	30	4	25	1	23
2XQD_Y	tRNA links to Rfam database...	0.34	0.37	0.32	10	2819	22	1	20	1	17
2ZZN_D	tRNA links to Rfam database...	0.61	0.63	0.61	17	2457	13	1	10	2	10
3A2K_C	tRNA links to Rfam database...	0.44	0.46	0.42	13	2895	18	2	16	0	15
3A3A_A	tRNA-Sec links to Rfam database...	0.89	0.86	0.91	32	3620	3	1	2	0	5
3AKZ_H	tRNA links to Rfam database...	0.40	0.43	0.39	12	2670	19	3	16	0	16
3AM1_B	-	0.93	0.89	0.97	31	3208	2	0	1	1	4
3AMU_B	tRNA links to Rfam database...	0.44	0.48	0.42	13	2972	18	2	16	0	14
3GCA_A	-	0.04	0.06	0.07	1	514	13	1	12	0	16
3GX2_A	SAM links to Rfam database...	0.47	0.48	0.48	19	4331	22	0	21	1	21
3IVN_B	Purine links to Rfam database...	0.39	0.39	0.40	12	2316	18	0	18	0	19
3IWN_A	c-di-GMP-I links to Rfam database...	0.19	0.21	0.18	7	4238	33	8	25	0	26
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.69	0.74	37	6853	14	0	13	1	17
3J0L_a	-	0.16	0.19	0.17	3	1110	15	1	14	0	13
3J0L_g	-	0.13	0.25	0.08	1	452	12	8	4	0	3
3J0L_7	-	-0.01	0.00	0.00	0	1206	19	4	15	0	17
3J0L_2	-	0.21	0.24	0.18	8	6172	39	7	29	3	25
3J16_L	tRNA links to Rfam database...	0.45	0.47	0.44	14	2743	19	1	17	1	16
3J20_0	tRNA links to Rfam database...	0.59	0.57	0.63	17	2823	12	1	9	2	13
3J2L_3	5S_rRNA links to Rfam database...	0.58	0.57	0.60	30	7825	23	2	18	3	23
3J3D_C	tRNA links to Rfam database...	0.42	0.43	0.43	12	2747	18	2	14	2	16
3J3E_7	5S_rRNA links to Rfam database...	0.40	0.39	0.42	21	7090	29	3	26	0	33
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.12	0.12	4	7470	46	3	26	17	29
3J3F_7	5S_rRNA links to Rfam database...	0.74	0.74	0.74	37	7210	17	2	11	4	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.13	0.17	0.11	6	12191	61	9	40	12	30
3JYV_7	tRNA links to Rfam database...	0.21	0.22	0.21	7	2817	26	0	26	0	25
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.24	0.17	8	12199	43	16	23	4	25
3JYX_3	5S_rRNA links to Rfam database...	0.41	0.52	0.33	14	6285	34	12	17	5	13
3KTW_C	-	0.40	0.40	0.43	17	4520	24	4	19	1	26
3LA5_A	Purine links to Rfam database...	0.32	0.32	0.34	11	2453	21	1	20	0	23
3NDB_M	-	0.23	0.23	0.24	14	9121	46	1	44	1	47
3NKB_B	-	0.56	0.58	0.56	15	1989	13	0	12	1	11
3O58_2	5S_rRNA links to Rfam database...	0.20	0.24	0.17	9	7208	44	5	38	1	29
3O58_3	5_8S_rRNA links to Rfam database...	0.22	0.26	0.19	9	12355	45	9	30	6	26
3PDR_A	ykoK links to Rfam database...	0.66	0.61	0.72	44	12819	19	0	17	2	28
3RKF_A	Purine links to Rfam database...	0.70	0.65	0.76	22	2182	7	1	6	0	12
3SD1_A	THF links to Rfam database...	0.33	0.33	0.35	14	3876	26	0	26	0	28
3U4M_B	-	0.59	0.59	0.59	22	3123	15	0	15	0	15
3ZEX_H	-	0.14	0.18	0.12	7	8987	52	14	37	1	31
3ZEX_G	-	0.00	0.00	0.00	0	16456	15	1	14	0	74
3ZEX_D	5S_rRNA links to Rfam database...	0.17	0.18	0.18	9	6970	42	4	38	0	40
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.21	0.28	11	14156	29	3	26	0	41
3ZEX_F	-	-0.01	0.00	0.00	0	2610	29	4	14	11	12
3ZND_W	tRNA links to Rfam database...	0.19	0.22	0.18	5	2975	26	1	22	3	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4ATO_G	-	0.30	0.30	0.33	3	519	8	0	6	2	7
4ENB_A	crcB links to Rfam database...	0.61	0.63	0.60	12	1255	8	2	6	0	7
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13
4FNJ_A	-	0.83	0.81	0.87	13	580	3	0	2	1	3
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.34	0.31	11	3450	25	0	25	0	21
4FRN_A	AdoCbl-variant links to Rfam database...	0.12	0.14	0.12	5	5110	38	1	35	2	31
4JF2_A	preQ1-II links to Rfam database...	0.66	0.68	0.66	21	2818	11	0	11	0	10
4JRC_A	-	0.20	0.22	0.21	5	1516	19	0	19	0	18

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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 HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

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

Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

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