Skip to main content

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.