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Table 4 Representative search times for K = 6

From: MICA: desktop software for comprehensive searching of DNA databases

Query

Chromosome 1

Human Genome

 

Time (sec)

Hits

Time (sec)

Hits

Nondegenerate 3-mers

1.1 [0.80]

6.96 × 106

14.8

8.90 × 107

Nondegenerate 4-mers

0.28 [0.16]

1.69 × 106

4.2

2.17 × 107

Nondegenerate 6-mers

0.043 [0.0032]

160,702

0.96

2.05 × 106

Nondegenerate 8-mers

0.079 [0.011]

16,631

1.6

213,099

Nondegenerate 15-mers

0.088 [0.0074]

1.39

1.8

5.81

Nondegenerate 30-mers

0.13 [0.0076]

1.03

1.8

1.24

Nondegenerate 100-mers

0.12 [0.0050]

1.01

1.7

1.02

Nondegenerate 1000-mers

0.094 [0.0023]

1.00

1.3

1.00

Alu 30-mer fragment

0.12 [0.0055]

1,130

2.5

14,041

GDGCHC (Bsp 1286I)

0.13 [0.031]

398,999

2.5

4,776,086

GCCNNNNNGGC (Bgl I)

0.44 [0.15]

44,761

6.2

520,776

ACNNNNGTAYC (Bae I)

1.40 [0.37]

20,243

21.1

259,837

  1. Both DNA strands were searched using K = 6. The queries and the procedure were as described in Table 3, except that each 3- or 4-mer was extended to a partially degenerate 6-mer.
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BMC Bioinformatics

ISSN: 1471-2105

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