Table 6 Open in new tab Impact of the...

Jscore threshold	PL-HHblits^a	PL-BLAST^b	PL-HMMER^c
0.99	0.9207	0.9426	0.7184	0.9047	0.9155	0.5327	0.9043	0.9188	0.5642
0.9	0.9268	0.9438	0.6952	0.9150	0.9190	0.5107	0.9152	0.9197	0.5416
0.8	0.9305	0.9451	0.6795	0.9168	0.9203	0.5017	0.9175	0.9213	0.5321
0.7	0.9341	0.9446	0.6651	0.9170	0.9200	0.4947	0.9194	0.9229	0.5240
0.6	0.9375	0.9464	0.6517	0.9175	0.9200	0.4889	0.9206	0.9239	0.5176
0.5	0.9411	0.9488	0.6393	0.9179	0.9198	0.4834	0.9214	0.9245	0.5128
0.4	0.9426	0.9502	0.6288	0.9181	0.9196	0.4789	0.9222	0.9248	0.5068
0.3	0.9436	0.9509	0.6201	0.9180	0.9193	0.4741	0.9226	0.9250	0.5026
0.2	0.9442	0.9514	0.6122	0.9175	0.9187	0.4703	0.9226	0.9248	0.4987
0.1	0.9448	0.9516	0.6026	0.9164	0.9174	0.4658	0.9216	0.9237	0.4935
0.0	0.9419	0.9484	0.5738	0.9117	0.9125	0.4504	0.9164	0.9185	0.4800

Jscore threshold	PL-HHblits^a	PL-BLAST^b	PL-HMMER^c
0.99	0.9207	0.9426	0.7184	0.9047	0.9155	0.5327	0.9043	0.9188	0.5642
0.9	0.9268	0.9438	0.6952	0.9150	0.9190	0.5107	0.9152	0.9197	0.5416
0.8	0.9305	0.9451	0.6795	0.9168	0.9203	0.5017	0.9175	0.9213	0.5321
0.7	0.9341	0.9446	0.6651	0.9170	0.9200	0.4947	0.9194	0.9229	0.5240
0.6	0.9375	0.9464	0.6517	0.9175	0.9200	0.4889	0.9206	0.9239	0.5176
0.5	0.9411	0.9488	0.6393	0.9179	0.9198	0.4834	0.9214	0.9245	0.5128
0.4	0.9426	0.9502	0.6288	0.9181	0.9196	0.4789	0.9222	0.9248	0.5068
0.3	0.9436	0.9509	0.6201	0.9180	0.9193	0.4741	0.9226	0.9250	0.5026
0.2	0.9442	0.9514	0.6122	0.9175	0.9187	0.4703	0.9226	0.9248	0.4987
0.1	0.9448	0.9516	0.6026	0.9164	0.9174	0.4658	0.9216	0.9237	0.4935
0.0	0.9419	0.9484	0.5738	0.9117	0.9125	0.4504	0.9164	0.9185	0.4800

Table 6

Impact of the Jscore threshold (cf. Equation (6)) on the three PL-based search methods on the SCOPe 2.06 benchmark dataset

Jscore threshold	PL-HHblits^a			PL-BLAST^b			PL-HMMER^c
Jscore threshold	ROC1^d	ROC50^d	Coverage^d	ROC1^d	ROC50^d	Coverage^d	ROC1^d	ROC50^d	Coverage^d
0.99	0.9207	0.9426	0.7184	0.9047	0.9155	0.5327	0.9043	0.9188	0.5642
0.9	0.9268	0.9438	0.6952	0.9150	0.9190	0.5107	0.9152	0.9197	0.5416
0.8	0.9305	0.9451	0.6795	0.9168	0.9203	0.5017	0.9175	0.9213	0.5321
0.7	0.9341	0.9446	0.6651	0.9170	0.9200	0.4947	0.9194	0.9229	0.5240
0.6	0.9375	0.9464	0.6517	0.9175	0.9200	0.4889	0.9206	0.9239	0.5176
0.5	0.9411	0.9488	0.6393	0.9179	0.9198	0.4834	0.9214	0.9245	0.5128
0.4	0.9426	0.9502	0.6288	0.9181	0.9196	0.4789	0.9222	0.9248	0.5068
0.3	0.9436	0.9509	0.6201	0.9180	0.9193	0.4741	0.9226	0.9250	0.5026
0.2	0.9442	0.9514	0.6122	0.9175	0.9187	0.4703	0.9226	0.9248	0.4987
0.1	0.9448	0.9516	0.6026	0.9164	0.9174	0.4658	0.9216	0.9237	0.4935
0.0	0.9419	0.9484	0.5738	0.9117	0.9125	0.4504	0.9164	0.9185	0.4800

Jscore threshold	PL-HHblits^a			PL-BLAST^b			PL-HMMER^c
Jscore threshold	ROC1^d	ROC50^d	Coverage^d	ROC1^d	ROC50^d	Coverage^d	ROC1^d	ROC50^d	Coverage^d
0.99	0.9207	0.9426	0.7184	0.9047	0.9155	0.5327	0.9043	0.9188	0.5642
0.9	0.9268	0.9438	0.6952	0.9150	0.9190	0.5107	0.9152	0.9197	0.5416
0.8	0.9305	0.9451	0.6795	0.9168	0.9203	0.5017	0.9175	0.9213	0.5321
0.7	0.9341	0.9446	0.6651	0.9170	0.9200	0.4947	0.9194	0.9229	0.5240
0.6	0.9375	0.9464	0.6517	0.9175	0.9200	0.4889	0.9206	0.9239	0.5176
0.5	0.9411	0.9488	0.6393	0.9179	0.9198	0.4834	0.9214	0.9245	0.5128
0.4	0.9426	0.9502	0.6288	0.9181	0.9196	0.4789	0.9222	0.9248	0.5068
0.3	0.9436	0.9509	0.6201	0.9180	0.9193	0.4741	0.9226	0.9250	0.5026
0.2	0.9442	0.9514	0.6122	0.9175	0.9187	0.4703	0.9226	0.9248	0.4987
0.1	0.9448	0.9516	0.6026	0.9164	0.9174	0.4658	0.9216	0.9237	0.4935
0.0	0.9419	0.9484	0.5738	0.9117	0.9125	0.4504	0.9164	0.9185	0.4800

^aPL-based search based on HHblits with the default parameters.

^bPL-based search based on PSI-BLAST with default parameters except that the iterations was set as five.

^cPL-based search based on JackHMMER with the default parameters.

^dPerformance at homology level that contains close homology and remote homology (belonging to the same SCOP superfamily).