Table 2

More results on synthetic yeast-like data. Same as Table 1, except that the sequences have five embedded motifs (drawn from weight matrices that had 80% "polarisation"); this better mimics real data and also improves the performance of all programs.

q = 0.35

q = 0.45

q = 0.55

q = 0.65


5 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

13266

0

0.44

0.00

29352

0

0.98

0.00

sigma-

0

0

0.00

N/A

456

0

0.02

0.00

19028

0

0.63

0.00

29274

0

0.98

0.00

dialign

78

0

0.03

0.00

60

0

0.02

0.00

2639

0

0.09

0.00

11383

40

0.38

0.00

alignm

3067

506

0.10

0.14

11389

2153

0.38

0.16

24496

1217

0.82

0.05

28687

305

0.96

0.01

clustalw

20814

9186

0.69

0.31

26730

3270

0.89

0.11

29341

659

0.98

0.02

29878

122

1.00

0.00

mlagan

17160

12840

0.57

0.43

26930

3070

0.90

0.10

29716

284

0.99

0.01

30000

0

1.00

0.00

tcoffee

10421

19579

0.35

0.65

20548

9452

0.68

0.32

28129

1871

0.94

0.06

29887

113

1.00

0.00

6

sigma+

0

0

0.00

N/A

1625

0

0.03

0.00

36055

28

0.60

0.00

58596

0

0.98

0.00

sigma-

452

42

0.01

0.09

5984

0

0.10

0.00

47264

26

0.79

0.00

58876

0

0.98

0.00

dialign

510

144

0.01

0.22

1719

74

0.03

0.04

10250

0

0.17

0.00

33979

0

0.57

0.00

alignm

3893

181

0.06

0.04

28300

1363

0.47

0.05

54487

1077

0.91

0.02

59496

170

0.99

0.00

clustalw

42116

17884

0.70

0.30

53797

6203

0.90

0.10

58316

1684

0.97

0.03

59613

387

0.99

0.01

mlagan

29458

30542

0.49

0.51

53833

6167

0.90

0.10

59427

573

0.99

0.01

60000

0

1.00

0.00

tcoffee

25878

34122

0.43

0.57

47767

12233

0.80

0.20

58708

1292

0.98

0.02

59975

25

1.00

0.00

9

sigma+

40

30

0.00

0.43

2300

0

0.03

0.00

56847

20

0.63

0.00

87436

0

0.97

0.00

sigma-

322

30

0.00

0.09

5805

0

0.06

0.00

69821

120

0.78

0.00

88775

0

0.99

0.00

dialign

450

80

0.01

0.15

2844

106

0.03

0.04

20179

0

0.22

0.00

59400

0

0.66

0.00

alignm

10165

652

0.11

0.06

60374

2420

0.67

0.04

85011

933

0.94

0.01

89651

201

1.00

0.00

clustalw

62461

27539

0.69

0.31

83233

6767

0.92

0.08

86738

3262

0.96

0.04

89167

833

0.99

0.01

mlagan

33857

56143

0.38

0.62

81225

8775

0.90

0.10

88869

1131

0.99

0.01

90000

0

1.00

0.00

tcoffee

43416

46584

0.48

0.52

76928

13072

0.85

0.15

89240

760

0.99

0.01

89990

10

1.00

0.00


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

Open Data