CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	Fold		Pknots
MCC	0.560	>	0.515
Average MCC ± 95% Confidence Intervals	0.514 ± 0.078	<	0.517 ± 0.077
Sensitivity	0.495	>	0.461
Positive Predictive Value	0.640	>	0.582
Total TP	951	>	886
Total TN	274631	>	274595
Total FP	624	<	708
Total FP CONTRA	59	<	68
Total FP INCONS	476	<	568
Total FP COMP	89	>	72
Total FN	972	<	1037
P-value	3.56938820447e-08

^top

Performance plots

Comparison of performance of Fold and Pknots. 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 Fold and Pknots).
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 Fold and Pknots).
Comparison of average Matthews Correlation Coefficients (MCCs) for Fold and Pknots. 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 Fold and Pknots).

^top

Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	951
Total TN	274631
Total FP	624
Total FP CONTRA	59
Total FP INCONS	476
Total FP COMP	89
Total FN	972

Total Scores
MCC	0.560
Average MCC ± 95% Confidence Intervals	0.514 ± 0.078
Sensitivity	0.495
Positive Predictive Value	0.640
Nr of predictions	56

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
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...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LKR_A	-	0.85	0.79	0.91	31	6071	5	0	3	2	8
2M58_A	-	-0.01	0.00	0.00	0	1638	15	0	15	0	17
2WWQ_V	tRNA links to Rfam database...	0.76	0.64	0.90	18	2906	3	0	2	1	10
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3ADB_C	-	0.80	0.74	0.88	28	4154	4	0	4	0	10
3AKZ_H	tRNA links to Rfam database...	0.84	0.75	0.95	21	2679	1	1	0	0	7
3AM1_B	-	0.78	0.71	0.86	25	3211	4	0	4	0	10
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	6864	7	1	6	0	22
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J0L_a	-	0.20	0.19	0.23	3	1115	10	2	8	0	13
3J0L_2	-	0.25	0.24	0.26	8	6185	25	2	21	2	25
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	0	5	0	14
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...	0.45	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...	0.47	0.43	0.52	12	2752	11	1	10	0	16
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7478	34	2	23	9	33
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.57	20	7105	15	1	14	0	34
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.28	0.29	10	12211	39	5	20	14	26
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.68	0.92	34	7223	4	0	3	1	16
3J3V_B	5S_rRNA links to Rfam database...	0.51	0.42	0.63	24	6983	14	1	13	0	33
3NDB_M	-	0.84	0.74	0.96	45	9133	3	0	2	1	16
3NKB_B	-	0.35	0.31	0.42	8	1997	11	0	11	0	18
3NPB_A	SAM links to Rfam database...	0.70	0.61	0.80	28	6986	10	1	6	3	18
3O58_3	5_8S_rRNA links to Rfam database...	0.29	0.31	0.28	11	12363	41	3	26	12	24
3O58_2	5S_rRNA links to Rfam database...	0.71	0.71	0.71	27	7222	12	3	8	1	11
3PDR_A	ykoK links to Rfam database...	0.77	0.64	0.94	46	12831	5	0	3	2	26
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...	0.57	0.48	0.69	20	3887	9	1	8	0	22
3U4M_B	-	0.45	0.35	0.59	13	3138	9	1	8	0	24
3UZL_B	tRNA links to Rfam database...	0.77	0.62	0.96	23	3546	1	0	1	0	14
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.85	0.75	0.97	30	4722	2	0	1	1	10
3ZEX_G	-	0.76	0.65	0.89	48	16417	12	0	6	6	26
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.67	0.87	33	6983	5	1	4	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...	0.22	0.21	0.24	11	14151	45	4	30	11	41
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	23	1	20	2	18
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.57	0.82	31	7102	7	1	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11744	43	5	27	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.32	0.30	0.38	3	520	5	1	4	0	7
4ENB_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1263	7	1	6	0	14
4ENC_A	crcB links to Rfam database...	0.31	0.26	0.38	5	1313	8	1	7	0	14
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.24	0.22	0.27	7	3460	19	3	16	0	25
4FRN_A	AdoCbl-variant links to Rfam database...	0.41	0.36	0.46	13	5123	15	2	13	0	23
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12
4JRC_A	-	0.29	0.26	0.35	6	1523	11	0	11	0	17

^top

Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	886
Total TN	274595
Total FP	708
Total FP CONTRA	68
Total FP INCONS	568
Total FP COMP	72
Total FN	1037

Total Scores
MCC	0.515
Average MCC ± 95% Confidence Intervals	0.517 ± 0.077
Sensitivity	0.461
Positive Predictive Value	0.582
Nr of predictions	56

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.67	0.58	0.79	23	5122	9	2	4	3	17
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.79	0.75	0.83	15	1522	3	1	2	0	5
2LKR_A	-	0.44	0.44	0.45	17	6067	22	4	17	1	22
2M58_A	-	0.51	0.41	0.64	7	1642	4	1	3	0	10
2WWQ_V	tRNA links to Rfam database...	0.24	0.21	0.29	6	2905	16	1	14	1	22
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3ADB_C	-	0.92	0.84	1.00	32	4154	0	0	0	0	6
3AKZ_H	tRNA links to Rfam database...	0.84	0.75	0.95	21	2679	1	1	0	0	7
3AM1_B	-	0.91	0.83	1.00	29	3211	0	0	0	0	6
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J0L_a	-	0.35	0.31	0.42	5	1116	7	1	6	0	11
3J0L_2	-	0.36	0.36	0.36	12	6183	23	3	18	2	21
3J0L_g	-	-0.01	0.00	0.00	0	460	5	2	3	0	4
3J16_L	tRNA links to Rfam database...	0.34	0.30	0.41	9	2753	13	0	13	0	21
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
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.51	0.75	27	7839	12	0	9	3	26
3J3D_C	tRNA links to Rfam database...	0.46	0.43	0.50	12	2751	12	1	11	0	16
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.06	0.08	2	7479	33	2	20	11	31
3J3E_7	5S_rRNA links to Rfam database...	0.43	0.35	0.54	19	7105	16	1	15	0	35
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.36	0.37	13	12211	34	2	20	12	23
3J3F_7	5S_rRNA links to Rfam database...	0.27	0.24	0.32	12	7222	27	1	25	1	38
3J3V_B	5S_rRNA links to Rfam database...	0.41	0.33	0.51	19	6984	18	1	17	0	38
3NDB_M	-	0.77	0.69	0.88	42	9132	7	1	5	1	19
3NKB_B	-	0.55	0.50	0.62	13	1995	8	0	8	0	13
3NPB_A	SAM links to Rfam database...	0.76	0.67	0.86	31	6985	8	1	4	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.27	0.31	0.24	11	12357	38	11	24	3	24
3O58_2	5S_rRNA links to Rfam database...	0.83	0.74	0.93	28	7230	3	0	2	1	10
3PDR_A	ykoK links to Rfam database...	0.54	0.44	0.65	32	12831	19	0	17	2	40
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.65	0.52	0.81	22	3889	5	0	5	0	20
3U4M_B	-	0.26	0.22	0.32	8	3135	17	0	17	0	29
3UZL_B	tRNA links to Rfam database...	0.75	0.59	0.96	22	3547	1	0	1	0	15
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.71	0.63	0.81	25	4722	7	0	6	1	15
3ZEX_G	-	0.36	0.32	0.41	24	16413	37	3	31	3	50
3ZEX_D	5S_rRNA links to Rfam database...	0.27	0.24	0.30	12	6981	28	0	28	0	37
3ZEX_H	-	0.20	0.21	0.20	8	9005	32	5	27	0	30
3ZEX_C	5_8S_rRNA links to Rfam database...	0.07	0.08	0.07	4	14141	54	4	47	3	48
3ZEX_F	-	0.00	0.00	0.00	0	2619	12	2	7	3	12
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.25	8	11749	36	3	21	12	25
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4ATO_G	-	0.30	0.30	0.33	3	519	6	2	4	0	7
4ENB_A	crcB links to Rfam database...	0.83	0.79	0.88	15	1258	2	1	1	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FNJ_A	-	-0.02	0.00	0.00	0	585	10	0	10	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.48	0.38	0.63	12	3467	7	0	7	0	20
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.42	0.63	15	5127	9	1	8	0	21
4JF2_A	preQ1-II links to Rfam database...	0.81	0.77	0.86	24	2822	4	3	1	0	7
4JRC_A	-	0.81	0.70	0.94	16	1523	1	1	0	0	7

^top

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 Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

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

Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

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