Optimization Profiles
Profiles apply to the profile engine (--engine profile).
Supported Hosts
| Host flag | Species | Codon table | Notes |
|---|---|---|---|
nbenthamiana (default) |
Nicotiana benthamiana | 3,876 SGN CDS | Stable. Recommended for agroinfiltration |
by2 ⚠️ Experimental |
N. tabacum BY-2 | 1,534 Kazusa CDS (2007) | Experimental. Uses N. tabacum codon usage as proxy. Not wet-lab validated for BY-2 expression. |
BY-2 host is experimental
The by2 host profile uses N. tabacum codon usage data as a proxy for Tobacco BY-2 suspension cells. It has not been wet-lab validated for BY-2 expression performance. Use for exploratory design only.
| Profile | Description |
|---|---|
balanced |
CAI + GC balance — default for most use cases |
high_cai |
Maximum codon adaptation index |
gc_target |
Target GC 42.5% for N. benthamiana |
viral_delivery |
Adjusted for TRV viral vector delivery |
Usage
factorforge optimize input.fasta -e profile -p balanced -o output.fasta
factorforge optimize input.fasta -e profile -p high_cai -o output.fasta
factorforge optimize input.fasta -e profile -p viral_delivery -o output.fasta
factorforge optimize input.fasta -e profile -p balanced --host by2 -o output.fasta
Python API
from factorforge.engines.profile.pipeline import OptimizationPipeline
pipeline = OptimizationPipeline(profile="high_cai")
result = pipeline.run("MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEG...")
Profile Selection Guide
- General expression →
balanced - Maximizing CAI →
high_cai - GC-sensitive downstream processes →
gc_target - Viral vector (TRV, TMV) →
viral_delivery