Table 1

Calibration of automated design pipeline with 8 manually-designed and experimentally-validated Southern blot probes.

Probe Name

Mouse Genomic Target

Length (bases)

Score ratio (self/second hit)

Second hit identity (%)

Second hit query coverage (%)

Repetitive & low-complexity DNA (%)


Dusp6_5prime_probe

Dusp6 (5')

946

30.1

71

8

3.2


SAP102_5prime_PDZ3_probe

Dlg3 (5')

969

27.2

72

8

2.7


Dusp6_3prime_probe

Dusp6 (3')

1004

29.4

61

13

4.5


Actb_probe

Actb

881

22.8

91

6

6.7


SAP102_3prime_probe

Dlg3 (3')

886

22.2

77

8

19.4


NR2B_probe

Grin2b

567

11.1

81

14

9.5


SAP102_5prime_probe

Dlg3

784

9.89

68

29

81.7


PSD-95_exon_9_probe

Dlg4 (exon 9)

296

3.3

76

54

nd


Average ± standard error

791.6 ± 85.9

19.5 ± 3.6

74.6 ± 3.2

17.5 ± 5.8

18.2 ± 10.8


Shown are the mouse genomic target and length of each of the probes, together with uniqueness and repetitive DNA content measures produced by evaluating the probes in the automated design pipeline. These are the score ratio, which is calculated as the ratio of the score of the on-target hit of the probe to the genomic locus of interest, and the highest-scoring off-target second best hit. The percentage repetitive and low-complexity DNA content (as estimated by RepeatMasker and DUST) is shown for each of the probes. Finally, the percentage identity and query coverage are given for the second hit used to calculate the score ratio.

Croning et al. BMC Genomics 2010 11:74   doi:10.1186/1471-2164-11-74

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