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		ProbKnot
MCC	0.782	>	0.708
Average MCC ± 95% Confidence Intervals	0.788 ± 0.094	>	0.737 ± 0.104
Sensitivity	0.691	<	0.733
Positive Predictive Value	0.893	>	0.696
Total TP	427	<	453
Total TN	31118	>	30945
Total FP	98	<	277
Total FP CONTRA	10	<	59
Total FP INCONS	41	<	139
Total FP COMP	47	<	79
Total FN	191	>	165
P-value	3.56938820447e-08

^top

Performance plots

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

^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	427
Total TN	31118
Total FP	98
Total FP CONTRA	10
Total FP INCONS	41
Total FP COMP	47
Total FN	191

Total Scores
MCC	0.782
Average MCC ± 95% Confidence Intervals	0.788 ± 0.094
Sensitivity	0.691
Positive Predictive Value	0.893
Nr of predictions	44

^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_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_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_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
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
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
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

^top

Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	453
Total TN	30945
Total FP	277
Total FP CONTRA	59
Total FP INCONS	139
Total FP COMP	79
Total FN	165

Total Scores
MCC	0.708
Average MCC ± 95% Confidence Intervals	0.737 ± 0.104
Sensitivity	0.733
Positive Predictive Value	0.696
Nr of predictions	44

^top

2. Individual counts for ProbKnot [ 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	-	0.85	0.86	0.86	6	268	3	0	1	2	1
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
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	-	0.89	0.86	0.93	25	2413	9	0	2	7	4
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
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_X	-	0.53	0.57	0.50	4	536	7	1	3	3	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	9	0	5	4	4
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_h	-	0.89	0.88	0.90	28	2109	3	0	3	0	4
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_g	-	-0.02	0.00	0.00	0	171	7	1	4	2	2
3J0L_a	-	0.60	0.64	0.58	7	399	6	4	1	1	4
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_2	-	0.30	0.31	0.31	8	2224	27	1	17	9	18
3J16_L	tRNA links to Rfam database...	0.42	0.48	0.38	10	1133	16	3	13	0	11
3NMU_E	-	-0.02	0.00	0.00	0	207	11	6	3	2	3
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	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...	1.00	1.00	1.00	12	142	0	0	0	0	0
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	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...	0.92	1.00	0.84	16	1274	11	3	0	8	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
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...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	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 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 ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

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