Table 3

Results on synthetic plasmodium-like data. Performance of various multiple sequence alignment programs on synthetic data generated with dinucleotide correlations that mimic the Plasmodium falciparum genome. See the caption of Table 1 for explanation of the column and row labels.

q = 0.35

q = 0.45

q = 0.55

q = 0.65


No embedded WM's


Ns

Prog

N+

N-

Sen

Er

N+

N-

Sen

Er

N+

N-

Sen

Er

N+

N-

Sen

Er


3

sigma+

0

0

0.00

N/A

0

0

0.00

N/A

1036

0

0.03

0.00

24617

0

0.82

0.00

sigma-

66

1070

0.00

0.94

9175

372

0.31

0.04

27959

0

0.93

0.00

29547

0

0.98

0.00

dialign

292

1471

0.01

0.83

800

1582

0.03

0.66

4185

929

0.14

0.18

14957

104

0.50

0.01

alignm

753

1563

0.03

0.67

5889

2085

0.20

0.26

20462

1846

0.68

0.08

27433

728

0.91

0.03

clustalw

12057

17943

0.40

0.60

23528

6472

0.78

0.22

27965

2035

0.93

0.07

29814

186

0.99

0.01

mlagan

7974

22026

0.27

0.73

21709

8291

0.72

0.28

29145

855

0.97

0.03

30000

0

1.00

0.00

tcoffee

6865

23135

0.23

0.77

15398

14602

0.51

0.49

25261

4739

0.84

0.16

29043

957

0.97

0.03

6

sigma+

0

0

0.00

N/A

48

0

0.00

0.00

8033

0

0.13

0.00

54293

0

0.90

0.00

sigma-

1684

8161

0.03

0.83

26675

4113

0.44

0.13

57619

86

0.96

0.00

59411

0

0.99

0.00

dialign

294

7229

0.00

0.96

3423

5362

0.06

0.61

15806

2521

0.26

0.14

46203

75

0.77

0.00

alignm

0

50

0.00

1.00

3678

237

0.06

0.06

42406

972

0.71

0.02

57938

610

0.97

0.01

clustalw

26172

33828

0.44

0.56

46240

13760

0.77

0.23

55270

4730

0.92

0.08

59234

766

0.99

0.01

mlagan

13737

46263

0.23

0.77

40430

19570

0.67

0.33

57668

2332

0.96

0.04

59931

69

1.00

0.00

tcoffee

19149

40851

0.32

0.68

40764

19236

0.68

0.32

56346

3654

0.94

0.06

59532

468

0.99

0.01


Siddharthan BMC Bioinformatics 2006 7:143   doi:10.1186/1471-2105-7-143

Open Data