Table 1

Results by PolyFreq and PolyBayes on eighteen data sets of EST sequences

Data set

Size

PolyBayes (trimmed)

PolyFreq (full length)

PolyBayes (full length)

TP

FP

FN

NSU

TP

FP

FN

NSU

TP

FP

FN

NSU

Hs.119589

4403

12

170

50

1491

5

24

57

4391

12

152

50

1531

Hs.129673

1665

7

48

11

1457

5

11

13

1662

T/A

Hs.148340

1603

3

36

9

1563

4

9

8

1583

3

67

9

1560

Hs.170622

1514

1

37

12

429

3

18

10

1507

2

73

11

365

Hs.178551

1685

5

62

12

1632

6

14

11

1676

T/A

Hs.180909

1017

3

50

6

983

3

20

6

1012

3

164

6

996

Hs.187199

2041

T/A

N/A

1997

T/A

Hs.198281

3156

9

110

22

3077

15

54

16

3149

T/A

Hs.350927

1017

5

42

11

976

9

21

7

1015

6

139

10

995

Hs.356331

1441

2

55

9

318

1

14

10

1436

2

85

9

239

Hs.356572

2822

0

46

2

2534

0

17

2

2821

T/A

Hs.439552

7163

T/A

N/A

6873

T/A

Hs.444467

4033

N/A

805

N/A

4028

N/A

679

Hs.446628

1490

4

32

12

1338

5

12

11

1486

T/A

Hs.520640

4120

T/A

9

52

27

4099

T/A

Hs.522463

8294

T/A

N/A

8280

T/A

Hs.524390

4462

T/A

9

48

24

4454

T/A

Hs.544577

7537

14

60

43

1716

10

17

47

7517

18

175

39

1556

The mark N/A means that no SNP from dbSNP was mapped to the anchor sequence because of lack of a RefSeq sequence. The mark T/A means that PolyBayes terminated abnormally without producing any output file. A candidate SNP from the program is considered as true positive (TP) if it is in dbSNP or false positive (FP) otherwise. A SNP from dbSNP that occurs in the data set is considered as false negative (FN) if it is not reported as a candidate SNP from the program. The number of sequences used (NSU) by the program in generation of candidate SNPs is reported.

Wang and Huang BMC Bioinformatics 2005 6:220   doi:10.1186/1471-2105-6-220