Table 1 Pairwise alignment results for the IsoBase dataset. Protein functionality is determined based on the KEGG Orthology (KO) group annotations

Yeast – Fly

Yeast – Worm

Yeast – Human

Yeast – Mouse

Fly – Worm

CN ^a

SPE ^b

CN

SPE

CN

SPE

CN

SPE

CN

SPE

CUFID-align

1,708

0.748

1,548

0.834

1,330

0.736

1,304

0.794

2,616

0.873

SMETANA-CSRW

1,610

0.757

1,426

0.850

1,224

0.733

1,192

0.802

2,444

0.870

SMETANA

1,530

0.733

1,422

0.843

1,134

0.710

1,182

0.782

2,338

0.852

PINALOG

1,368

0.722

640

0.737

1,100

0.682

76

0.400

672

0.689

HubAlign

1,326

0.681

98

0.170

1,082

0.633

42

0.231

102

0.201

IsoRank

1,414

0.712

650

0.703

1,142

0.702

76

0.369

918

0.818

BLAST-MWBM^c

1,712

0.776

1,544

0.836

1,334

0.768

1,280

0.792

2,680

0.885

Fly – Human

Fly – Mouse

Worm – Mouse

Worm – Human

Human – Mouse

CN

SPE

CN

SPE

CN

SPE

CN

SPE

CN

SPE

CUFID-align

2,528

0.754

2,364

0.788

1,818

0.807

1,858

0.791

5,178

0.983

SMETANA-CSRW

2,358

0.763

2,146

0.768

1,610

0.811

1,722

0.803

5,002

0.978

SMETANA

2,096

0.706

2,112

0.764

1,578

0.803

1,570

0.780

4,876

0.972

PINALOG

1,172

0.604

118

0.567

66

0.458

482

0.677

282

0.972

HubAlign

354

0.219

34

0.230

24

0.188

32

0.063

144

0.667

IsoRank

1,736

0.725

146

0.566

72

0.456

644

0.793

286

0.979

BLAST-MWBM

2,580

0.766

2,374

0.781

1,824

0.808

1,884

0.794

5,140

0.982