Table 2

Detection of PRS with different t parameter in the three reference datasets

9644_GSS_EMBL

9693_WGS_Sanger

9644_simGSS_Sanger

t

1

2

3

4

5

6

1

2

3

4

5

1

2

3

4

5

# PRS

###

330

121

39

21

10

500

57

21

12

10

415

30

18

10

7

# no hits

42

19

7

4

3

1

10

1

0

0

0

0

0

0

0

0

# 1 hit

###

225

78

21

12

5

366

25

2

0

0

300

5

1

0

0

# 2 hits

94

33

7

2

0

0

40

6

1

0

0

34

0

0

0

0

#>2 hits

128

53

29

12

6

4

84

25

18

12

10

81

25

17

10

7

#>30 hits

19

11

9

5

3

3

13

8

8

8

8

19

14

11

9

7

The number of PRSs found by ReRep with different t parameter for the three datasets is given in the first line (#PRS). The detected PRSs of each individual run are BLASTed against the whole genome sequence (e-value e^-20). The number of hits is reported in the following lines: # no hit and # 1 hit indicates false positives. # > 2 hits indicate PRSs occurring more than twice in the genome. # > 30 hits indicates highly repetitive PRSs. An l parameter of 400 was used.

Otto et al. BMC Bioinformatics 2008 9:366   doi:10.1186/1471-2105-9-366