Table 8 Open in new tab The impact of...

\|${\beta}_2$\|	PL-HHblits^a	PL-BLAST^b	PL-HMMER^c
0	0.8684	0.8966	59.4196	0.1593	0.8157	0.8261	49.2459	0.1932	0.8109	0.8180	50.6132	0.1903
0.5	0.8685	0.8968	59.4602	0.1596	0.8153	0.8260	49.4026	0.1940	0.8111	0.8178	50.6957	0.1886
0.6	0.8685	0.8969	59.4658	0.1596	0.8153	0.8260	49.4271	0.1940	0.8111	0.8178	50.7016	0.1886
0.7	0.8688	0.8970	59.4765	0.1600	0.8153	0.8260	49.5291	0.1940	0.8111	0.8179	50.7594	0.1886
0.8	0.8690	0.8973	59.6349	0.1601	0.8153	0.8263	49.5385	0.1941	0.8112	0.8181	50.7648	0.1888
0.9	0.8689	0.8973	59.6375	0.1602	0.8154	0.8262	49.5561	0.1936	0.8112	0.8182	50.7772	0.1890
1.0	0.8689	0.8972	59.8296	0.1607	0.8158	0.8268	49.8555	0.1942	0.8112	0.8182	50.8469	0.1901
1.1	0.8690	0.8976	59.8305	0.1608	0.8158	0.8268	49.8559	0.1942	0.8114	0.8181	50.8510	0.1899
1.2	0.8688	0.8982	59.8465	0.1611	0.8157	0.8269	49.8670	0.1943	0.8114	0.8181	50.8533	0.1903
1.3	0.8688	0.8987	59.8570	0.1612	0.8158	0.8269	49.8679	0.1942	0.8114	0.8181	50.8436	0.1905
1.4	0.8687	0.8988	59.9074	0.1613	0.8158	0.8268	49.8742	0.1942	0.8119	0.8182	50.8473	0.1904
1.5	0.8687	0.8988	59.9074	0.1613	0.8158	0.8268	49.8742	0.1942	0.8119	0.8182	50.8473	0.1904

|${\beta}_2$|

PL-HHblits^a

PL-BLAST^b

PL-HMMER^c

ROC1^d

ROC50^d

EPQ^d

ROC1^d

ROC50^d

TP^d

EPQ^d

ROC1^d

ROC50^d

TP^d

EPQ^d

0.8684

0.8966

59.4196

0.1593

0.8157

0.8261

49.2459

0.1932

0.8109

0.8180

50.6132

0.1903

0.5

0.8685

0.8968

59.4602

0.1596

0.8153

0.8260

49.4026

0.1940

0.8111

0.8178

50.6957

0.1886

0.6

0.8685

0.8969

59.4658

0.1596

0.8153

0.8260

49.4271

0.1940

0.8111

0.8178

50.7016

0.1886

0.7

0.8688

0.8970

59.4765

0.1600

0.8153

0.8260

49.5291

0.1940

0.8111

0.8179

50.7594

0.1886

0.8

0.8690

0.8973

59.6349

0.1601

0.8153

0.8263

49.5385

0.1941

0.8112

0.8181

50.7648

0.1888

0.9

0.8689

0.8973

59.6375

0.1602

0.8154

0.8262

49.5561

0.1936

0.8112

0.8182

50.7772

0.1890

1.0

0.8689

0.8972

59.8296

0.1607

0.8158

0.8268

49.8555

0.1942

0.8112

0.8182

50.8469

0.1901

1.1

0.8690

0.8976

59.8305

0.1608

0.8158

0.8268

49.8559

0.1942

0.8114

0.8181

50.8510

0.1899

1.2

0.8688

0.8982

59.8465

0.1611

0.8157

0.8269

49.8670

0.1943

0.8114

0.8181

50.8533

0.1903

1.3

0.8688

0.8987

59.8570

0.1612

0.8158

0.8269

49.8679

0.1942

0.8114

0.8181

50.8436

0.1905

1.4

0.8687

0.8988

59.9074

0.1613

0.8158

0.8268

49.8742

0.1942

0.8119

0.8182

50.8473

0.1904

1.5

0.8687

0.8988

59.9074

0.1613

0.8158

0.8268

49.8742

0.1942

0.8119

0.8182

50.8473

0.1904

\|${\beta}_2$\|	PL-HHblits^a	PL-BLAST^b	PL-HMMER^c
0	0.8684	0.8966	59.4196	0.1593	0.8157	0.8261	49.2459	0.1932	0.8109	0.8180	50.6132	0.1903
0.5	0.8685	0.8968	59.4602	0.1596	0.8153	0.8260	49.4026	0.1940	0.8111	0.8178	50.6957	0.1886
0.6	0.8685	0.8969	59.4658	0.1596	0.8153	0.8260	49.4271	0.1940	0.8111	0.8178	50.7016	0.1886
0.7	0.8688	0.8970	59.4765	0.1600	0.8153	0.8260	49.5291	0.1940	0.8111	0.8179	50.7594	0.1886
0.8	0.8690	0.8973	59.6349	0.1601	0.8153	0.8263	49.5385	0.1941	0.8112	0.8181	50.7648	0.1888
0.9	0.8689	0.8973	59.6375	0.1602	0.8154	0.8262	49.5561	0.1936	0.8112	0.8182	50.7772	0.1890
1.0	0.8689	0.8972	59.8296	0.1607	0.8158	0.8268	49.8555	0.1942	0.8112	0.8182	50.8469	0.1901
1.1	0.8690	0.8976	59.8305	0.1608	0.8158	0.8268	49.8559	0.1942	0.8114	0.8181	50.8510	0.1899
1.2	0.8688	0.8982	59.8465	0.1611	0.8157	0.8269	49.8670	0.1943	0.8114	0.8181	50.8533	0.1903
1.3	0.8688	0.8987	59.8570	0.1612	0.8158	0.8269	49.8679	0.1942	0.8114	0.8181	50.8436	0.1905
1.4	0.8687	0.8988	59.9074	0.1613	0.8158	0.8268	49.8742	0.1942	0.8119	0.8182	50.8473	0.1904
1.5	0.8687	0.8988	59.9074	0.1613	0.8158	0.8268	49.8742	0.1942	0.8119	0.8182	50.8473	0.1904

Table 8

Open in new tab

The impact of parameter |${\beta}_2$| on the three PL-search methods on the SCOP 1.59 benchmark dataset

\|${\beta}_2$\|	PL-HHblits^a			PL-BLAST^b				PL-HMMER^c
\|${\beta}_2$\|	ROC1^d	ROC50^d	TP	EPQ^d	ROC1^d	ROC50^d	TP^d	EPQ^d	ROC1^d	ROC50^d	TP^d	EPQ^d
0	0.8684	0.8966	59.4196	0.1593	0.8157	0.8261	49.2459	0.1932	0.8109	0.8180	50.6132	0.1903
0.5	0.8685	0.8968	59.4602	0.1596	0.8153	0.8260	49.4026	0.1940	0.8111	0.8178	50.6957	0.1886
0.6	0.8685	0.8969	59.4658	0.1596	0.8153	0.8260	49.4271	0.1940	0.8111	0.8178	50.7016	0.1886
0.7	0.8688	0.8970	59.4765	0.1600	0.8153	0.8260	49.5291	0.1940	0.8111	0.8179	50.7594	0.1886
0.8	0.8690	0.8973	59.6349	0.1601	0.8153	0.8263	49.5385	0.1941	0.8112	0.8181	50.7648	0.1888
0.9	0.8689	0.8973	59.6375	0.1602	0.8154	0.8262	49.5561	0.1936	0.8112	0.8182	50.7772	0.1890
1.0	0.8689	0.8972	59.8296	0.1607	0.8158	0.8268	49.8555	0.1942	0.8112	0.8182	50.8469	0.1901
1.1	0.8690	0.8976	59.8305	0.1608	0.8158	0.8268	49.8559	0.1942	0.8114	0.8181	50.8510	0.1899
1.2	0.8688	0.8982	59.8465	0.1611	0.8157	0.8269	49.8670	0.1943	0.8114	0.8181	50.8533	0.1903
1.3	0.8688	0.8987	59.8570	0.1612	0.8158	0.8269	49.8679	0.1942	0.8114	0.8181	50.8436	0.1905
1.4	0.8687	0.8988	59.9074	0.1613	0.8158	0.8268	49.8742	0.1942	0.8119	0.8182	50.8473	0.1904
1.5	0.8687	0.8988	59.9074	0.1613	0.8158	0.8268	49.8742	0.1942	0.8119	0.8182	50.8473	0.1904

\|${\beta}_2$\|	PL-HHblits^a			PL-BLAST^b				PL-HMMER^c
\|${\beta}_2$\|	ROC1^d	ROC50^d	TP	EPQ^d	ROC1^d	ROC50^d	TP^d	EPQ^d	ROC1^d	ROC50^d	TP^d	EPQ^d
0	0.8684	0.8966	59.4196	0.1593	0.8157	0.8261	49.2459	0.1932	0.8109	0.8180	50.6132	0.1903
0.5	0.8685	0.8968	59.4602	0.1596	0.8153	0.8260	49.4026	0.1940	0.8111	0.8178	50.6957	0.1886
0.6	0.8685	0.8969	59.4658	0.1596	0.8153	0.8260	49.4271	0.1940	0.8111	0.8178	50.7016	0.1886
0.7	0.8688	0.8970	59.4765	0.1600	0.8153	0.8260	49.5291	0.1940	0.8111	0.8179	50.7594	0.1886
0.8	0.8690	0.8973	59.6349	0.1601	0.8153	0.8263	49.5385	0.1941	0.8112	0.8181	50.7648	0.1888
0.9	0.8689	0.8973	59.6375	0.1602	0.8154	0.8262	49.5561	0.1936	0.8112	0.8182	50.7772	0.1890
1.0	0.8689	0.8972	59.8296	0.1607	0.8158	0.8268	49.8555	0.1942	0.8112	0.8182	50.8469	0.1901
1.1	0.8690	0.8976	59.8305	0.1608	0.8158	0.8268	49.8559	0.1942	0.8114	0.8181	50.8510	0.1899
1.2	0.8688	0.8982	59.8465	0.1611	0.8157	0.8269	49.8670	0.1943	0.8114	0.8181	50.8533	0.1903
1.3	0.8688	0.8987	59.8570	0.1612	0.8158	0.8269	49.8679	0.1942	0.8114	0.8181	50.8436	0.1905
1.4	0.8687	0.8988	59.9074	0.1613	0.8158	0.8268	49.8742	0.1942	0.8119	0.8182	50.8473	0.1904
1.5	0.8687	0.8988	59.9074	0.1613	0.8158	0.8268	49.8742	0.1942	0.8119	0.8182	50.8473	0.1904

^aRepresents PL-HHblits with β₁ value of 0.8 (cf. Algorithm 1).

^bRepresents PL-BLAST with β₁ value of 0.95 (cf. Algorithm 1).

^cRepresents PL-HMMER with β₁ value of 0.95 (cf. Algorithm 1).

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

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