Skip to main content

Table 2 Execution time in seconds for the comparison of the sequences listed in Table 1 under “pairwise comparison” (lowest execution time and memory consumption of each row are highlighted in bold). The comparison of mammalian chromosomes was also included to test the ability of GECKO and reference software packages to function when analysing very large datasets. The dictionary calculation time is included in the reported times, since the dictionary were not pre-calculated. “n.a.” indicates that resource problems prevented analysis execution and the presence of (*1) after some execution times indicates that the time was measured in a bigger machine because in such cases they were using more than 8GB of memory (more details of these cases in the Additional file 1 Section 3.3)

From: Breaking the computational barriers of pairwise genome comparison

 

Gepard

MUMmer

Mauve

Comparison

Time

Memory

Time

Memory

Time

Memory

TYLCV-TYLCV-lr2

0.84

52824

0.00

2944

0.06

2800

BuchneraAPS-BuchneraBp

2.56

74808

0.44

11100

6.73

14304

E.colik12-E.coliO157

33.12

378412

10.63

79212

45.92

99880

D.Melanogaster-D.Pseudoobscura

238.34

716244

45.99

355272

294.92

379912

H.Sapiens-Chr1-P.Troglodytes-chr1

7 0 8 4 . 0 0 1

49788208

23226.001

15747168

>604800.00

n.a.

 

LASTZ

LAST

GECKO

Comparison

Time

Memory

Time

Memory

Time

Memory

TYLCV-TYLCV-lr2

0.04

67388

0.00

3024

0.36

1564816

BuchneraAPS-BuchneraBp

0.46

71244

46.20

475912

1.60

1564816

E.colik12-E.coliO157

1.83

95884

109.00

1972028

17.20

1564816

D.Melanogaster-D.Pseudoobscura

19.64

190448

1593.00

5436716

48.72

1564816

H.Sapiens-Chr1-P.Troglodytes-chr1

78360.00

5782352

n.a.

312065840

11848.15

1564816