Automated design of genomic Southern blot probes

BMC Genomics

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.

ISSN: 1471-2164