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Table 4 Comparison of performance with human chromosome X - mouse chromosome X pair.

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

 

length (bp)

Sn (%)

time

memory (GB)

Blastz (default)

41,649,203

58.9

117 m 03 s

2.8

Blastz (T = 2 C = 2)

21,094,947

36.5

15 m 21 s

2.8

Blastz* (T = 2 C = 2)

32,684,714

58.0

23 m 22 s

0.4

NUCmer

1,299,148

5.4

4 m 01 s

2.3

Cgaln (-X2500 k = 11)

25,675,191

54.4

5 m 56 s

0.9

Cgaln (-X2500 k = 12)

27,776,861

56.0

4 m 21 s

1.2

  1. Performance of alignment programs examined on human chromosome X (chrX) vs. mouse chromosome X. The threshold T col was set to "-X2500".
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BMC Bioinformatics

ISSN: 1471-2105

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