CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		TurboFold(20)
MCC	0.691	>	0.655
Average MCC ± 95% Confidence Intervals	0.679 ± 0.109	>	0.670 ± 0.108
Sensitivity	0.544	>	0.529
Positive Predictive Value	0.881	>	0.816
Total TP	288	>	280
Total TN	74040	>	74024
Total FP	49	<	82
Total FP CONTRA	0	<	5
Total FP INCONS	39	<	58
Total FP COMP	10	<	19
Total FN	241	<	249
P-value	2.02510705504e-08

Comparison of performance of PPfold(20) and TurboFold(20). 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 PPfold(20) and TurboFold(20)).
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 PPfold(20) and TurboFold(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and TurboFold(20). 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 PPfold(20) and TurboFold(20)).

Total Scores
MCC	0.691
Average MCC ± 95% Confidence Intervals	0.679 ± 0.109
Sensitivity	0.544
Positive Predictive Value	0.881
Nr of predictions	15

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...	0.63	0.45	0.90	9	980	1	0	1	0	11
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
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	0	0	0	0	9
3J2L_3	5S_rRNA links to Rfam database...	0.78	0.62	0.97	33	7841	3	0	1	2	20
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.21	0.52	11	14175	12	0	10	2	41
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.71	0.92	35	6983	3	0	3	0	14
4A1C_3	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.56	0.95	18	3467	1	0	1	0	14

Total Scores
MCC	0.655
Average MCC ± 95% Confidence Intervals	0.670 ± 0.108
Sensitivity	0.529
Positive Predictive Value	0.816
Nr of predictions	15

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...	0.92	0.90	0.95	18	971	1	0	1	0	2
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
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...	0.66	0.57	0.77	17	2828	6	0	5	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.74	0.58	0.94	31	7842	5	0	2	3	22
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...	0.59	0.48	0.74	20	3889	7	1	6	0	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	14	14171	14	2	9	3	38
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.63	0.91	31	6987	3	0	3	0	18
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	28	0	19	9	28
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.