Table 2

Runtimes and internal space requirements for finding MUMs. We compared MUMmer 3.19 [8], MGA [9], and SeqAn for different DNA sequences on a 3.2 GHz Intel Xeon computer with 3 GB of internal memory running Linux. Because MUMmer finds MUMs of not more than two sequences, its results on the Chlamydia and Escherichia coli strains are left empty. For the last dataset, we used SeqAn's external memory data strutures to limit the internal memory consumption.

Species

MUMer

MGA

SeqAn

size (Mbp)

time (m:s)

space (MB)

time (m:s)

space (MB)

time (m:s)

space (MB)


C. trachomatis D/UW-3/CX

1.043

C. muridarum Nigg

1.073

-

-

0:06

33.8

0:04

31.6

C. trachomatis A/HAR-13

1.044

E. coli K12

4.640

E. coli O157:H7 str. Sakai

5.498

E. coli CFT073

5.231

-

-

105:40

353.5

0:58

304.6

E. coli UTI89

5.066

E. coli 536

4.939

E. coli APEC O1

5.082

H. sapiens (chr. 21)

46.94

2:25

568

4:44

1188

4:06

1307

M. musculus (chr. 16)

98.25

H. sapiens (chr. 16)

98.25

2:55

1362

18:48

1500

5:38

1627

P. troglodytes (chr. 16)

88.83

external string


H. sapiens (chr. 1)

247.2

insufficient memory

insufficient memory

66:20

510

M. musculus (chr. 1)

197.1


Döring et al. BMC Bioinformatics 2008 9:11   doi:10.1186/1471-2105-9-11

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