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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.
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BMC Bioinformatics

ISSN: 1471-2105

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