Schematic of the ArrayOligoSelector oligonucleotide-selection algorithm. Oligonucleotide selection begins with the collection of all possible 70 mer oligonucleotides from a given ORF. Four filters are executed in parallel: selection for uniqueness within the genome, an optional user-defined pattern filter, avoidance of significant secondary structure (self-binding), and avoidance of low-complexity sequence. The intersection of the set of all oligonucleotides passing these filters are then further selected for a desired base composition and then ranked by proximity to the 3' end of the ORF.
Bozdech et al. Genome Biology 2003 4:R9 doi:10.1186/gb-2003-4-2-r9