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	IPknot		CentroidHomfold‑LAST
MCC	0.760	>	0.704
Average MCC ± 95% Confidence Intervals	0.783 ± 0.083	>	0.750 ± 0.098
Sensitivity	0.747	>	0.628
Positive Predictive Value	0.777	<	0.794
Total TP	723	>	608
Total TN	100524	<	100688
Total FP	322	>	230
Total FP CONTRA	66	>	43
Total FP INCONS	141	>	115
Total FP COMP	115	>	72
Total FN	245	<	360
P-value	3.56938820447e-08

^top

Performance plots

Comparison of performance of IPknot and CentroidHomfold-LAST. 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 CentroidHomfold‑LAST).
Comparison of performance of IPknot and CentroidHomfold-LAST. 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 CentroidHomfold‑LAST).
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 CentroidHomfold‑LAST).
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 CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and CentroidHomfold-LAST. 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 CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and CentroidHomfold-LAST. 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 CentroidHomfold‑LAST).

^top

Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	723
Total TN	100524
Total FP	322
Total FP CONTRA	66
Total FP INCONS	141
Total FP COMP	115
Total FN	245

Total Scores
MCC	0.760
Average MCC ± 95% Confidence Intervals	0.783 ± 0.083
Sensitivity	0.747
Positive Predictive Value	0.777
Nr of predictions	49

^top

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_X	-	1.00	1.00	1.00	7	537	3	0	0	3	0
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
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_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
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_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
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
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_D	5S_rRNA links to Rfam database...	0.81	0.80	0.82	28	2762	10	0	6	4	7
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
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
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
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

^top

Performance of CentroidHomfold‑LAST - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

Total Base Pair Counts
Total TP	608
Total TN	100688
Total FP	230
Total FP CONTRA	43
Total FP INCONS	115
Total FP COMP	72
Total FN	360

Total Scores
MCC	0.704
Average MCC ± 95% Confidence Intervals	0.750 ± 0.098
Sensitivity	0.628
Positive Predictive Value	0.794
Nr of predictions	49

^top

2. Individual counts for CentroidHomfold‑LAST [ 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	517	11	0	11	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	0.84	0.73	1.00	8	154	0	0	0	0	3
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	-	0.00	0.00	0.00	0	2436	4	0	4	0	29
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_X	-	1.00	1.00	1.00	7	537	0	0	0	0	0
2YIE_Z	-	1.00	1.00	1.00	8	594	0	0	0	0	0
3AMU_B	tRNA links to Rfam database...	0.95	0.95	0.95	18	1138	4	0	1	3	1
3J0L_7	-	0.83	0.70	1.00	7	512	1	0	0	1	3
3J0L_g	-	0.00	0.00	0.00	0	176	0	0	0	0	2
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_2	-	0.55	0.31	1.00	8	2242	0	0	0	0	18
3J0L_a	-	-0.01	0.00	0.00	0	408	3	1	2	0	11
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J0L_h	-	0.88	0.84	0.93	27	2111	4	0	2	2	5
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_0	tRNA links to Rfam database...	0.41	0.52	0.34	11	1187	22	7	14	1	10
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2C_M	-	0.51	0.31	0.83	30	39889	12	0	6	6	66
3J2C_O	-	0.00	0.00	0.00	0	3987	0	0	0	0	41
3J2L_3	5S_rRNA links to Rfam database...	0.94	0.94	0.94	32	2986	8	0	2	6	2
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.77	0.66	0.90	19	1512	2	1	1	0	10
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	144	0	0	0	0	2
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	-	0.78	0.73	0.84	16	1257	4	0	3	1	6
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	0.88	1.00	29	1960	1	0	0	1	4
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.83	0.91	29	2764	8	0	3	5	6
3ZEX_G	-	0.97	0.93	1.00	42	6465	10	0	0	10	3
3ZEX_E	-	0.00	0.00	0.00	0	8273	33	9	22	2	34
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	29	8	8	13	15
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	7	0	6	1	8
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	1	0	0	1	8
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...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.43	0.50	0.40	12	1172	18	6	12	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	0.37	0.46	0.32	13	1807	28	11	17	0	15
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

^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 IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

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

Performance of CentroidHomfold‑LAST - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

2. Individual counts for CentroidHomfold‑LAST [ download as .csv ]