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Table 3 Comparison of performance with human chromosome 20 - mouse chromosome 2 pair.

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

  length (bp) Sn (%) Sp mam (%) time memory (GB)
Blastz (default) 18,598,895 85.9 57.5 66 m 40 s 1.6
Blastz (T = 2 C = 2) 16,353,601 85.1 95.5 9 m 45 s 1.6
Blastz* (T = 2 C = 2) 16,665,937 85.3 80.8 12 m 20 s 0.4
NUCmer 1,118,494 5.8 75.2 3 m 55 s 1.0
Cgaln (-X2500 k = 11) 13,964,626 79.2 92.3 2 m 14 s 0.8
Cgaln (-X2500 k = 12) 15,154,530 81.4 90.6 2 m 16 s 1.1
  1. Performance of alignment programs examined on human chromosome 20 (chr20) vs. mouse chromosome 2 (chr2). The row of Blastz with the symbol "*" refers to the examination on split chromosomal sequences. The threshold T col was set to "-X2500". Sp mam is evaluated as the ratio of the coverage with human chr20 - mouse chr2 to that with the human chr20 - whole-genome sequence of mouse.