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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.