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	CentroidHomfold‑LAST		RNAshapes
MCC	0.708	>	0.667
Average MCC ± 95% Confidence Intervals	0.752 ± 0.089	>	0.729 ± 0.084
Sensitivity	0.629	<	0.680
Positive Predictive Value	0.803	>	0.661
Total TP	651	<	704
Total TN	102789	>	102535
Total FP	239	<	489
Total FP CONTRA	43	<	96
Total FP INCONS	117	<	265
Total FP COMP	79	<	128
Total FN	384	>	331
P-value	3.56938820447e-08

^top

Performance plots

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

^top

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

1. Total counts & total scores for CentroidHomfold‑LAST

Total Base Pair Counts
Total TP	651
Total TN	102789
Total FP	239
Total FP CONTRA	43
Total FP INCONS	117
Total FP COMP	79
Total FN	384

Total Scores
MCC	0.708
Average MCC ± 95% Confidence Intervals	0.752 ± 0.089
Sensitivity	0.629
Positive Predictive Value	0.803
Nr of predictions	56

^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
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LA5_A	-	0.77	0.71	0.83	5	269	1	0	1	0	2
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
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.23	0.06	1.00	1	905	0	0	0	0	17
2YIE_Z	-	1.00	1.00	1.00	8	594	0	0	0	0	0
2YIE_X	-	1.00	1.00	1.00	7	537	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_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
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
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_a	-	-0.01	0.00	0.00	0	408	3	1	2	0	11
3J0L_2	-	0.55	0.31	1.00	8	2242	0	0	0	0	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...	0.41	0.52	0.34	11	1187	22	7	14	1	10
3J2C_O	-	0.00	0.00	0.00	0	3987	0	0	0	0	41
3J2C_M	-	0.51	0.31	0.83	30	39889	12	0	6	6	66
3J2L_3	5S_rRNA links to Rfam database...	0.94	0.94	0.94	32	2986	8	0	2	6	2
3NMU_E	-	0.57	0.33	1.00	1	215	3	0	0	3	2
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
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_E	-	0.00	0.00	0.00	0	8273	33	9	22	2	34
3ZEX_G	-	0.97	0.93	1.00	42	6465	10	0	0	10	3
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.83	0.91	29	2764	8	0	3	5	6
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

Performance of RNAshapes - scored lower in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	704
Total TN	102535
Total FP	489
Total FP CONTRA	96
Total FP INCONS	265
Total FP COMP	128
Total FN	331

Total Scores
MCC	0.667
Average MCC ± 95% Confidence Intervals	0.729 ± 0.084
Sensitivity	0.680
Positive Predictive Value	0.661
Nr of predictions	56

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LA5_A	-	0.77	0.71	0.83	5	269	3	0	1	2	2
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
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
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	-	1.00	1.00	1.00	29	2411	6	0	0	6	0
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
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.33	0.43	0.27	3	533	11	3	5	3	4
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
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	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J0L_2	-	0.46	0.46	0.48	12	2225	20	1	12	7	14
3J16_L	tRNA links to Rfam database...	0.59	0.57	0.63	12	1140	7	0	7	0	9
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...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J2C_O	-	0.43	0.44	0.44	18	3946	27	3	20	4	23
3J2C_M	-	0.61	0.65	0.58	62	39818	68	17	28	23	34
3J2L_3	5S_rRNA links to Rfam database...	0.77	0.79	0.75	27	2984	14	1	8	5	7
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
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	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.43	0.50	0.38	8	1272	17	4	9	4	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.58	0.63	19	1959	12	2	9	1	14
3ZEX_E	-	-0.01	0.00	0.00	0	8247	59	20	37	2	34
3ZEX_G	-	0.66	0.67	0.67	30	6462	27	4	11	12	15
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.80	0.93	28	2766	6	0	2	4	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	11	16	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	7	0	4	3	6
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
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
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 CentroidHomfold‑LAST - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

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

Performance of RNAshapes - scored lower in this pairwise comparison

1. Total counts & total scores for RNAshapes

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