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Table 3 Results obtained with designed probes for a mixture of phenanthrene and fluoranthene.

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

A

B

A

B

A

B

A

B

A

B

A

B

A

B

Total number of

specific probes

256

384

48

128

128

1024

1024

768

768

384

128

128

576

768

1024

512

Number of specific

probes giving a positive

signal (SNR' > 3)

1

2

0

1

3

1

2

1

4

1

1

1

3

1

0

0

Highest median SNR'

obtained for each

targeted region

18.32

±

3.64

6.62

±

0.31

X

22.64

±

3.21

8.61

±

1.59

9.93

±

1.32

8.92

±

1.52

16.26

±

2.45

5.79

±

1.73

4.09

±

0.66

4.47

±

0.30

4.54

±

0.81

36.87

±

7.83

9.79

±

1.39

X

X

Specific probe for

EPA505 gene giving

highest median SNR'

Yes

No

No

Yes

No

Yes

Yes

Yes

Yes

No

Yes

No

Yes

Yes

No

No

For comparison, total

number of specific probes

giving a positive signal

with glucose

0

0

0

0

0

0

1

0

0

0

0

0

0

0

0

0

  1. For each degenerate probe defined targeting two different regions (A and 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), highest median SNR' visualized for each targeted region of each gene and whether the probe specific to the strain EPA505 gene gives this highest signal median SNR'.