Figure 2

Schematic overview of C ODNS. Here our method CODNS is applied to choose codons in a portion of two parental genes so as to produce a 9 nt "run" of common nucleotides, likely to be sufficient for a cross-over between complementary strands. To achieve the run, we use a combination of silent DNA substitutions (underlined) as well as a conservative amino acid substitution (boxed). The implications of these choices can be global; e.g., TTC for F and CTC for L would end the current run at 7 nt, but provide the first 2 nt of a new one. Our dynamic programming algorithm finds the globally optimal solution.