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Table 1 Time and space requirements of MUMmer 2.1 and 3.0 when computing all exact matches of length 20 or longer for different pairs of sequences

From: Versatile and open software for comparing large genomes

Reference genome

Query genome

MUMmer 2.1

MUMmer 3.0

Species

Size (Mbp)

Species

Size (Mbp)

Time (sec)

Space (MB)

Time (sec)

Space (MB)

E. coli K12

4.6

E. coli O157:H7

5.5

18

102

17

77

A. fumigatus

28.0

A. nidulans

30.1

128

578

120

459

Saccharomyces cerevisiae

13.0

Schizosaccharomyces pombe

13.8

51

261

47

204

D. melanogaster (chromosome 2L)

22.2

D. pseudoobscura (all chromosomes)

150.0

546

684

520

485

Homo sapiens (chromosome 21)

44.7

Mus musculus (chromosome 16)

99.2

-

-

430

759

  1. Timings were done on a Linux-based computer with a 2.4 GHz Pentium processor. The human-mouse comparison was run only with MUMmer 3.0. Mbp, millions of base pairs; MB, megabytes. A suffix tree is constructed only for the reference genome.