Design of a combinatorial DNA microarray for protein-DNA interaction studies

BMC Bioinformatics

Table 2 Using array replicates to discover the Rap1 binding site when the flanking sequence is involved in binding.

Flanking/Primer Sequence^a	\|\|xxxxxxxxxxx xxxxxxxxxxxxxxxx primer combinatorial	\|\|xxxxxxCACCC xxxxxxxxxxxxxxxx primer combinatorial
Total # of Probes Bound	29	744
Top BioProspector Hits (1 ^st n)	CACCCATACA (34)	ATTCATGCTC (1)
# of Replicate Probes Bound	28	59
Top BioProspector Hits (1 ^st n)	CACCCATACA (37)	CACCCATACA (25)

^a The first array design contains a flanking primer sequence that does not contain any part of the binding site. In the second array design, the last 5 bases of the flanking primer sequence (shown in bold) constitute half of the consensus Rap1 binding site.

ISSN: 1471-2105