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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.
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BMC Bioinformatics

ISSN: 1471-2105

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