Algorithm.

Procedure PrimerDesign(m, G, L↱, L↰)

(* L↱, L↰ represent lengths of the two regions *)

1. Let (* Initial estimate *)

2. )

(* Return sub-graph induced by () with Delta;↱ (Δ↰) edges per forward (reverse) primer and optimal coverage. *)

3. Compute Δc = MaxAdjacency()

4. Use Welsh and Powell algorithm [Welsh and Powell, 1967] to color (and ). Return m↱ (and, m↰) colors.

5. If |m – m↱ · m↰| is large, adjust Δ↱, Δ↰; Go to Step 2.