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Table 4 Results obtained with designed probes with total DNA extracted from the contaminated soil S3.

From: Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

Gene name

phnA1a

phnA2a

ahdA1c

ahdA2c

bphB

bphC

bphA3

ahdA4

Targeted region

A

B

B

A

B

A

B

B

A

Total number of

specific probes

256

128

1024

1024

768

768

128

768

1024

Number of specific

probes giving a

positive signal

(SNR' > 3)

0

37

204

18

1

36

16

44

2

Percentage of probes

giving a positive

signal (SNR' > 3)

0

28.90

19.92

1.75

0.13

4.68

12.50

5.72

0.19

Highest median SNR'

obtained for each

targeted region

0

±

0.00

9.47

±

0.70

42.85

±

5.83

7.05

±

1.37

4.29

±

1.71

6.33

±

2.05

4.43

±

1.31

8.84

±

2.15

3.48

±

0.98

  1. For each degenerate probe defined targeting one particular region (A or B) of genes (phnA1a, phnA2a, ahdA1c, ahdA2c, bphB, bphC, bphA3 and ahdA4), total number of specific probes stemming from the degenerate sequence, total number of specific probes giving a 'positive' signal (with a SNR' > 3), probe percentage giving a 'positive' signal and highest signal median SNR' visualized for each targeted region of each gene.