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Table 1. Parameters, computation times and memory consumption of programs applied to selected genome pairs.

From: Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

Program

Parameters (and abbreviation)

Running time (user and system) in seconds

Memory consumption in Mb

HSP/MUM determination

   

NCBI-BLASTN

(ncbiblastn)

25.79

165.92

WU-BLASTN

(wublastn)

896.79

904.69

BLASTZ

K=2000 (blastz2000)

48.11

125.73

 

K=2500 (blastz2500)

47.80

124.39

 

K=3000 (blastz3000)

47.64

123.19

 

K=3500 (blastz3500)

47.61

122.45

BLAT

-minScore=0 − minIdentity=0 − tileSize=8 (blatminTS)

2,134.54

2443.43

 

-minScore=0 − minIdentity=0 (blatmin)

178.15

174.78

 

-minScore=30 − minIdentity=50 (BLAT)

177.05

167.41

 

-minScore=30 − minIdentity=90 (blatid90)

177.08

167.41

MUMmer

-l 20 -mum (mum20)

13.74

94.84

 

-l 30 -mum (mum30)

13.76

94.52

 

-l 40 -mum (mum40)

13.77

94.31

 

-l 50 -mum (mum50)

13.72

94.17

 

-l 20 -mumreference (ref20)

13.80

93.44

 

-l 30 -mumreference (ref30)

13.81

93.44

 

-l 40 -mumreference (ref40)

13.79

93.44

 

-l 50 -mumreference (ref50)

13.75

93.44

 

-l 20 -maxmatch (max20)

14.07

93.44

 

-l 30 -maxmatch (max30)

13.95

93.44

 

-l 40 -maxmatch (max40)

13.86

93.44

 

-l 50 -maxmatch (max50)

13.88

93.44

Distance calculation with GBDP (all formulas in each case)

   

tr F-2

mean, all programs

6,169.98

1836.62

cov F-2

 

22.22

424.68

tr NF

 

6,178.77

1853.68

cov NF

 

22.51

404.98

tr F-2

mean, all programs except MUMmer

39.54

415.04

cov F-2

 

12.18

229.58

tr NF

 

111.19

506.07

cov NF

 

19.78

235.64

tr F-2

mean, NCBI-BLASTN only

155.83

732.63

cov F-2

 

34.89

465.39

tr NF

 

206.68

942.36

cov NF

 

43.13

473.68

tr F-2

mean, MUMmer only

11,278.68

3021.26

cov F-2

 

30.60

587.26

tr NF

 

11,235.07

2976.68

cov NF

 

24.78

546.09

  1. Performance of HSP/MUM determination programs under distinct settings (parameters are given if deviating from the default) and the subsequent distance calculation with GBDP. Abbreviations: cov, coverage distances; tr, greedy-with-trimming distances; F-2, filtering using an e-value threshold of 10−2; NF, no filtering.