Optimizing sequences

[TimothyStiles]

Before a sequence is synthesized it should be optimized in at least 3 ways that I can think of.

• Codon optimization for a target organism
• Non-repetitive parts optimization for a target organism
• Synthesis optimization (optimizing sequence for probability of synthesis success)

Each optimization would have its own function but it'd be great to eventually have a function that performs a suite of pre-synthesis optimizations and checks.

@Koeng101 has already written a little about codon optimization and synthesis optimization but we've yet to start working on non-repetitive parts optimization. Are there any other pre-synthesis optimizations that we should be considering?

[Koeng101]

Non-repetitive parts optimization for a target organism

The best way to do this is to take the target organism + your sequence of interest and building a suffix array / LCP array for them together. Then, you just look for large LCPs.