Skip to main content

Table 3 Number of detections per Mbp, average length, and average divergence for TRF, Mreps, Sputnik, STAR, and RepeatMasker, in the genome of four species.

From: Detecting microsatellites within genomes: significant variation among algorithms

  

HS

DM

NC

SC

  

All

Imperfect

   

detection number

      
 

TRF {2,7,7;20}

2425

512

3119

2902

1822

 

Mreps 1

1368

1084

1653

1371

879

 

Sputnik {1,-6,7}

6589

361

7475

7665

5712

 

STAR

395

260

311

343

182

 

RepeatMasker

256

179

207

230

104

average length

      
 

TRF {2,7,7;20}

16.07

28.84

14.24

14.61

13.85

 

Mreps 1

22.96

24.99

20.04

20.93

20.28

 

Sputnik {1,-6,7}

9.74

19.83

9.39

9.35

8.98

 

STAR

39.89

49.80

31.07

32.86

33.12

 

RepeatMasker

53.97

64.93

48.52

45.80

54.88

average divergence

      
 

TRF {2,7,7;20}

1.60

7.59

1.61

1.47

1.35

 

Mreps 1

12.39

15.65

11.46

10.10

11.71

 

Sputnik {1,-6,7}

0.44

7.96

0.46

0.38

0.32

 

STAR

7.45

11.33

7.98

6.44

7.59

 

RepeatMasker

8.40

11.97

13.42

9.31

13.14

  1. Both imperfect and all (perfect plus imperfect) detections are provided for the human genome while all detections only are reported for the other genomes. HS = Homo sapiens, SC = Saccharomyces cerevisiae, DM = Drosophila melanogaster, NC = Neurospora crassa. Divergence is deduced from the alignment of the detected sequence with the perfectly repeated corresponding sequence of focal consensus motif:
  2. divergence = (substitutions + insertions + deletions)/alignment length).
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us