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Table 1 Accuracy and Confidence values of local alignment

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

Data set

 

30 PAM

  

60 PAM

 

Matrix

Gap open

Gap extention

Accuracy

Confi-dence

Gap open

Gap extention

Accuracy

Confi-dence

PAM30

19.0

0.2

0.9672

0.9883

8.0

1.0

0.6768

0.8781

PAM60

16.0

0.2

0.9776

0.9881

14.0

0.2

0.8635

0.9507

PAM120

10.0

0.1

0.9816

0.9876

10.0

0.5

0.9244

0.9519

PAM250

8.0

0.1

0.9821

0.9862

11.0

0.2

0.9353

0.9489

Blosum45

10.0

0.1

0.9803

0.9861

14.0

0.2

0.9246

0.9439

Blosum50

14.0

0.1

0.9802

0.9862

13.0

0.5

0.9227

0.9436

Blosum62

13.0

0.1

0.9802

0.9862

17.0

0.5

0.9216

0.9479

Gonnet250

8.0

0.1

0.9828

0.9862

10.0

0.2

0.9329

0.9437

Gonnet_p

7.0

0.1

0.9852

0.9839

8.0

0.1

0.9390

0.9336

Optima

9.0

0.1

0.9814

0.9861

17.0

0.5

0.9138

0.9421

VTML250

9.0

0.1

0.9808

0.9854

11.0

0.1

0.9293

0.9426

MIQS

10.0

0.1

0.9813

0.9860

12.0

0.2

0.9287

0.9433

Pfasum050

10.0

0.1

0.9808

0.9860

14.0

0.2

0.9271

0.9444

Pfasum100

10.0

0.1

0.9800

0.9864

12.0

0.2

0.9200

0.9452

Crooks

11.0

0.1

0.9777

0.9859

14.0

0.2

0.9098

0.9457

CCF53

10.0

0.2

0.9796

0.9862

12.0

0.2

0.9195

0.9453

Moll60

11.0

0.1

0.9793

0.9862

11.0

0.5

0.9142

0.9440

Johnson

15.0

0.1

0.9795

0.9866

17.0

0.5

0.9139

0.9465

Prlic

16.0

0.1

0.9811

0.9853

21.0

0.1

0.9251

0.9394

Blake

23.0

0.1

0.9797

0.9841

25.0

1.0

0.9188

0.9318

Benner

8.0

0.2

0.9803

0.9834

10.0

0.1

0.9197

0.9316

Miyazawa

15.0

0.1

0.9749

0.9821

17.0

0.2

0.8941

0.9307

Data set

 

120 PAM

  

Bali Base

 

Matrix

Gap open

Gap extention

Accuracy

Confi-dence

Gap open

Gap extention

Accuracy

Confi-dence

PAM30

3.0

1.0

0.1648

0.2826

4.0

1.0

0.3207

0.4471

PAM60

4.0

1.0

0.2781

0.4016

3.0

2.0

0.3928

0.5026

PAM120

6.0

1.0

0.5310

0.6969

7.0

0.5

0.4823

0.5624

PAM250

12.0

0.5

0.7251

0.8039

8.0

0.5

0.5427

0.5821

Blosum45

13.0

0.5

0.6514

0.7664

10.0

0.5

0.5621

0.6121

Blosum50

11.0

1.0

0.6244

0.7482

11.0

0.5

0.5494

0.6050

Blosum62

12.0

1.0

0.5794

0.7378

11.0

0.5

0.5375

0.6019

Gonnet250

11.0

0.5

0.7210

0.7769

8.0

1.0

0.5779

0.6103

Gonnet_p

11.0

0.1

0.7659

0.7538

7.0

0.1

0.6433

0.6338

Optima

10.0

0.5

0.6424

0.7352

9.0

0.5

0.5625

0.6107

VTML250

11.0

0.5

0.7212

0.7757

6.0

1.0

0.5719

0.6025

MIQS

12.0

0.5

0.6969

0.7660

9.0

0.5

0.5729

0.6079

Pfasum050

13.0

0.5

0.6731

0.7602

10.0

0.5

0.5668

0.6090

Pfasum100

9.0

0.5

0.5849

0.7343

7.0

0.5

0.5384

0.5958

Crooks

7.0

1.0

0.4902

0.6733

8.0

0.5

0.5206

0.5958

CCF53

9.0

0.5

0.5819

0.7395

8.0

0.2

0.5358

0.5980

Moll60

7.0

1.0

0.5314

0.6721

8.0

0.5

0.5289

0.6003

Johnson

8.0

2.0

0.4898

0.6623

12.0

0.5

0.5122

0.5917

Prlic

19.0

1.0

0.6714

0.7377

16.0

1.0

0.5741

0.6098

Blake

25.0

4.0

0.6781

0.7396

21.0

1.0

0.5762

0.6016

Benner

12.0

0.5

0.6296

0.6877

8.0

0.5

0.5215

0.5480

Miyazawa

11.0

1.0

0.4928

0.6324

10.0

1.0

0.4826

0.5395