Figure 1

The flowchart of OligoRankPick. All possible oligonucleotides were extracted form the input sequence and stored. Subsequently four parameters of all possible oligonucleotides were calculated including the BLAST score to a second genomic target (uniqueness), the GC content (Tm), the Reverse Smith-Waterman score (self-binding) and the LZ compression score (sequence complexity). In the rank transformation step, the oligonucleotides are ranked based on each parameter and ordinal rank number is given to all oligonucleotides in each parameter rank independently. Finally weighted rank-sum (RS_(x)) is calculated for all oligonucleotides with uniqueness weights (W_BLAST), GC content weights (W_GC) self-binding weights (W_SW), and sequence complexity weights (W_LZ) and R_BLAST, R_GC, R_SR and R_LZ representing the ranks corresponding to each parameter ranking. Multiple RS_(x) are determined by the gene specific optimization using multiple weight sets (not indicated) and the lowest value is finally considered. The optimal candidate is selected based on the lowest RS_(x) amongst all oligonucleotides in the locus.