CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MaxExpect		Pknots
MCC	0.785	>	0.737
Average MCC ± 95% Confidence Intervals	0.780 ± 0.063	>	0.767 ± 0.062
Sensitivity	0.791	>	0.760
Positive Predictive Value	0.787	>	0.723
Total TP	1306	>	1255
Total TN	92053	>	91978
Total FP	570	<	661
Total FP CONTRA	82	<	151
Total FP INCONS	272	<	329
Total FP COMP	216	>	181
Total FN	345	<	396
P-value	3.56938820447e-08

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Performance plots

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

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Performance of MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP	1306
Total TN	92053
Total FP	570
Total FP CONTRA	82
Total FP INCONS	272
Total FP COMP	216
Total FN	345

Total Scores
MCC	0.785
Average MCC ± 95% Confidence Intervals	0.780 ± 0.063
Sensitivity	0.791
Positive Predictive Value	0.787
Nr of predictions	96

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.94	0.94	0.94	17	449	2	0	1	1	1
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2KU0_A	-	-0.04	0.00	0.00	0	283	9	1	8	0	12
2KUR_A	K10_TLS links to Rfam database...	0.95	0.95	0.95	18	448	1	0	1	0	1
2KUU_A	K10_TLS links to Rfam database...	0.94	0.94	0.94	17	429	2	0	1	1	1
2KUV_A	K10_TLS links to Rfam database...	0.94	0.95	0.95	18	420	1	0	1	0	1
2KUW_A	K10_TLS links to Rfam database...	0.94	0.94	0.94	17	452	2	0	1	1	1
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	0.93	0.88	1.00	7	142	0	0	0	0	1
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
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...	-0.03	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
2LI4_A	-	1.00	1.00	1.00	14	175	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	-	0.84	0.83	0.86	24	2412	11	0	4	7	5
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
2WRQ_Y	tRNA links to Rfam database...	0.94	0.89	1.00	8	1144	14	0	0	14	1
2WW9_D	-	0.08	0.10	0.08	1	729	15	2	9	4	9
2WW9_E	-	-0.03	0.00	0.00	0	168	5	0	4	1	5
2WW9_F	-	0.64	0.75	0.60	6	102	4	1	3	0	2
2WWQ_V	tRNA links to Rfam database...	0.97	0.95	1.00	18	1186	3	0	0	3	1
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	26	0	6	20	3
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.24	0.26	0.25	9	2009	28	1	26	1	26
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	6	1	3	2	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3AKZ_H	tRNA links to Rfam database...	1.00	1.00	1.00	20	1107	2	0	0	2	0
3AM1_B	-	0.86	0.86	0.86	25	1437	4	0	4	0	4
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	4
3GX2_A	SAM links to Rfam database...	0.93	0.89	0.96	25	1423	2	1	0	1	3
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.80	0.79	0.81	22	1445	6	1	4	1	6
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	8	0	5	3	3
3J0L_h	-	0.93	0.88	1.00	28	2112	2	0	0	2	4
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_7	-	-0.02	0.00	0.00	0	507	12	3	9	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_2	-	0.30	0.31	0.31	8	2224	25	2	16	7	18
3J16_L	tRNA links to Rfam database...	0.34	0.33	0.37	7	1140	12	0	12	0	14
3JYV_7	tRNA links to Rfam database...	0.48	0.45	0.53	9	1094	9	3	5	1	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.55	0.83	0.37	10	4729	34	14	3	17	2
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	24	0	4	20	3
3KTW_C	-	0.72	0.72	0.72	18	1755	14	2	5	7	7
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NDB_M	-	0.94	0.93	0.95	41	3671	7	0	2	5	3
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	-0.02	0.00	0.00	0	208	10	5	3	2	3
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	10	0	6	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.40	0.50	0.33	11	4731	36	8	14	14	11
3O58_2	5S_rRNA links to Rfam database...	0.91	0.94	0.88	29	2721	11	0	4	7	2
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	0	0	0	0	0
3PDR_A	ykoK links to Rfam database...	0.92	0.90	0.94	45	4792	5	1	2	2	5
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	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...	0.70	0.69	0.71	20	1505	8	3	5	0	9
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
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	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	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	8	0	0	8	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.81	0.86	30	2728	7	0	5	2	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	10	17	14	15
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	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10

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Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	1255
Total TN	91978
Total FP	661
Total FP CONTRA	151
Total FP INCONS	329
Total FP COMP	181
Total FN	396

Total Scores
MCC	0.737
Average MCC ± 95% Confidence Intervals	0.767 ± 0.062
Sensitivity	0.760
Positive Predictive Value	0.723
Nr of predictions	96

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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
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KRL_A	-	0.79	0.83	0.76	19	1999	13	5	1	7	4
2KU0_A	-	-0.04	0.00	0.00	0	282	10	0	10	0	12
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	-0.04	0.00	0.00	0	144	5	0	5	0	8
2KZL_A	-	0.66	0.69	0.64	9	506	6	2	3	1	4
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	0.96	0.93	1.00	13	226	0	0	0	0	1
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
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...	0.83	0.83	0.83	15	510	3	2	1	0	3
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
2LI4_A	-	1.00	1.00	1.00	14	175	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	-	0.48	0.55	0.43	16	2403	23	9	12	2	13
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.38	0.27	0.60	3	202	3	0	2	1	8
2RRC_A	-	0.92	0.86	1.00	6	69	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2WW9_D	-	0.52	0.60	0.46	6	728	13	5	2	6	4
2WW9_E	-	0.79	0.80	0.80	4	167	3	0	1	2	1
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WWQ_V	tRNA links to Rfam database...	0.29	0.32	0.29	6	1183	16	3	12	1	13
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.21	0.27	0.17	3	1817	33	3	12	18	8
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.32	0.34	0.32	12	2008	26	1	24	1	23
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.70	0.67	0.75	12	890	6	0	4	2	6
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
3A2K_C	tRNA links to Rfam database...	0.50	0.55	0.48	12	1083	13	3	10	0	10
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3AKZ_H	tRNA links to Rfam database...	1.00	1.00	1.00	20	1107	2	0	0	2	0
3AM1_B	-	1.00	1.00	1.00	29	1437	0	0	0	0	0
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	3	0	0	3	0
3GX2_A	SAM links to Rfam database...	0.55	0.57	0.55	16	1420	14	4	9	1	12
3IAB_R	-	1.00	1.00	1.00	12	373	4	0	0	4	0
3IVN_B	Purine links to Rfam database...	0.91	0.87	0.95	20	882	1	0	1	0	3
3IWN_A	c-di-GMP-I links to Rfam database...	0.22	0.21	0.25	6	1448	18	2	16	0	22
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3J0L_h	-	0.67	0.66	0.70	21	2110	11	4	5	2	11
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J0L_7	-	0.38	0.50	0.31	5	503	12	3	8	1	5
3J0L_g	-	-0.02	0.00	0.00	0	171	5	3	2	0	2
3J0L_2	-	0.44	0.46	0.43	12	2222	23	1	15	7	14
3J16_L	tRNA links to Rfam database...	0.41	0.43	0.41	9	1137	13	1	12	0	12
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_4	5_8S_rRNA links to Rfam database...	0.33	0.58	0.19	7	4720	41	22	7	12	5
3JYX_3	5S_rRNA links to Rfam database...	0.37	0.53	0.27	8	2348	26	17	5	4	7
3KTW_C	-	0.63	0.68	0.59	17	1751	18	3	9	6	8
3LA5_A	Purine links to Rfam database...	0.94	0.88	1.00	22	932	0	0	0	0	3
3NDB_M	-	0.92	0.93	0.91	41	3669	8	3	1	4	3
3NKB_B	-	0.64	0.68	0.62	13	714	8	0	8	0	6
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3NPB_A	SAM links to Rfam database...	0.84	0.81	0.88	30	2244	9	0	4	5	7
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.45	0.24	10	4722	39	18	14	7	12
3O58_2	5S_rRNA links to Rfam database...	0.93	0.90	0.97	28	2725	3	0	1	2	3
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	0	0	0	0	0
3PDR_A	ykoK links to Rfam database...	0.64	0.64	0.65	32	4791	19	4	13	2	18
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3R9X_C	-	0.87	0.88	0.88	7	221	5	0	1	4	1
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.78	0.76	0.81	22	1506	5	1	4	0	7
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	-	0.33	0.36	0.32	8	1251	17	4	13	0	14
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	7	0	0	7	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2723	30	4	25	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	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 MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

2. Individual counts for MaxExpect [ 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 ]