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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'.