Automated design of genomic Southern blot probes

BMC Genomics

Table 2 Comparison of manually-designed (calibration) and automatically-designed Southern blot probes.

Probe set	Length (bases)	Average score ratio (self/second hit)	Average repetitive & low-complexity DNA (%)	Unique hit to genome	Passed empirical selection criteria
Calibration (n = 8)	791.6 ± 85.9	19.5 ± 10.8	18.2 ± 10.8	0/8	3/8
Automated (n = 124)	818.1 ± 25.0	23.7 ± 1.3	4.1 ± 1.0*	62/86	103/134

Shown are the average length (± standard error) of the probes in the calibration and automatically designed sets, together with their average 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 average combined percentage repetitive and low-complexity DNA content (as estimated by RepeatMasker and DUST) is shown for each of the probes. Also shown are the number of probes in each set that had a unique hit to their target genomic locus, with no off-target hits i.e. no apparent cross-reactivity. * p < 0.05 Student's t-test.

ISSN: 1471-2164