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Optimization Profiles

Profiles apply to the profile engine (--engine profile).

Supported Hosts

Host flag Species Codon table Notes
nbenthamiana (default) Nicotiana benthamiana NbeV1.1 high-confidence CDS-derived current software default; legacy Kazusa/SGN composite retained as historical comparator Stable sequence-level design profile for agroinfiltration workflows; in-silico default only, not wet-lab validation or yield prediction
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.

Stable Profiles

These four profiles are fully supported and available via CLI, Python API, web app, and MCP. high_cai is N. benthamiana-only (see Supported Hosts above) — it is rejected for other hosts at the CLI, REST API, and web app.

Profile Description
balanced CAI + GC balance — default for most sequence-design reviews
high_cai CAI-focused synonymous CDS candidate. N. benthamiana-only; rejected for other hosts.
gc_target Targets a configurable GC percentage, defaulting to the active host GC-band midpoint (currently 43.5% for the NbeV1.1 HC CDS-derived N. benthamiana software default). Pass an explicit target to drive GC higher or lower.
assembly_friendly Golden Gate / MoClo workflows — avoids BsaI/BpiI Type IIS restriction sites via synonymous substitution. Does not yet score local GC uniformity or repeat patterns.

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 gc_target -o output.fasta
factorforge optimize input.fasta -e profile -p assembly_friendly -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

  • Default N. benthamiana CDS design → balanced
  • CAI-focused comparison → high_cai
  • GC-sensitive downstream processes → gc_target (pass an explicit GC target if you need a value other than the host midpoint)
  • Golden Gate / MoClo assembly → assembly_friendly

Not Public API

The following profiles are not part of the public API or MCP interface and are not supported for general use. They may change or be removed without notice.

Profile Status Notes
viral_delivery Not public Adjusted for TRV viral vector delivery. Not validated.
ramp Not public 5′ ramp design heuristic. Under development.