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Table 3 The ratio of local and global alignment quality parameters on 120 PAM test suite sequences and Balibase sequences

From: The ranging of amino acids substitution matrices of various types in accordance with the alignment accuracy criterion

Matrix

120 PAM

Balibase

Global / Local

Global / Local

Accuracy

Confidence

Accuracy

Confidence

PAM30

4.8938

2.8277

1.9510

1.3901

PAM60

2.9392

2.0120

1.6041

1.2407

PAM120

1.5422

1.1698

1.3035

1.1033

PAM250

1.1481

1.0251

1.1627

1.0720

Blosum45

1.2203

1.0249

1.1555

1.0575

Blosum50

1.2692

1.0513

1.1873

1.0633

Blosum62

1.3759

1.0676

1.2154

1.0724

Gonnet250

1.1275

1.0345

1.1407

1.0718

Gonnet_p

1.0275

1.0253

1.0058

1.0024

Optima

1.5409

1.3453

1.6990

1.5589

VTML250

1.1245

1.0335

1.1443

1.0765

MIQS

1.1545

1.0397

1.1377

1.0658

Pfasum050

1.1908

1.0443

1.1643

1.0685

Pfasum100

1.3631

1.0746

1.2123

1.0908

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BMC Bioinformatics

ISSN: 1471-2105

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