|
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 |
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| Reference genome |
Query genome |
MUMmer 2.1 |
MUMmer 3.0 |
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|
|
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| Species |
Size (Mbp) |
Species |
Size (Mbp) |
Time (sec) |
Space (MB) |
Time (sec) |
Space (MB) |
|
|
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| 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 |
|
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. | |||||||
Kurtz et al. Genome Biology 2004 5:R12 doi:10.1186/gb-2004-5-2-r12 |
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