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Table 1 Comparison of performance with E. coli CFT073 -E. coli K12 pair.

From: Cgaln: fast and space-efficient whole-genome alignment

  length (bp) Sn (%) Sp (%) time (s) memory (MB)
Blastz (default) 5,643,656 97.4 44.4 72 348
Blastz (T = 2 C = 2) 4,035,271 95.3 60.0 22 346
AVID 4,044,527 94.7 59.3 147 2297
NUCmer 1,121,714 26.1 59.2 12 90
Cgaln (-X4000) 4,313,795 96.3 57.2 9 167
  1. Comparison of the performance of Cgaln with other programs for E. coli CFT073 vs. E. coli K12. The length indicates the total length of generated HSPs. Sn and Sp indicate sensitivity and specificity, respectively. "-X4000" of Cgaln indicates that the threshold T col was set at 4000.