Total codons
N/AEvaluated sense codons📥 Sequence Input
or
Sequence Input Area
0
bp
GC:
0%
⚠️ Invalid characters are reported and must be corrected.
ℹ️ DNA coding sequence detected.
FactorForge preserves the translated protein while redesigning synonymous codons for the selected host and constraints.
🕒 Recent Designs
🛡️ All history is stored locally in your browser.
⚙️ Design Setup
Selected workflow settings
Preserve protein identity · host GC policy · pre-synthesis sequence checks
Testing: baseline and structure-conditioned design
Both modes use this form. 3DP requires uploaded coordinates and explicit position review.
🔬 3DP Cloud Pipeline: In Active Development
Automated AlphaFold cloud GPU folding is currently in active development. For research partners and experimental pilot testing, manual exact-match PDB/mmCIF structure upload is supported below.
Optional: PDB / mmCIF structure upload and position review
Upload a structure, request suggestions if available, and review your selected positions.
1DP selected: standard production sequence design.
Execution Mode
ML modes are an experimental preview while model development continues.
v2.1 recommended
✨ Recommended: 3-axis DP with 5′ initiation ramp awareness (nt 1–45 clamped 20–29% GC), homopolymer veto (≤5 nt).
Show experimental objectives not enabled
Codon Reference
Current production default only; comparator assets are retained for provenance and controlled analysis, not public selection.
Current default: NbeV1.1 HC CDS-derived i NbeV1.1 high-confidence CDS-derived codon usage is the configured in-silico software default for N. benthamiana. It is not experimental validation or comparative biological-performance evidence.
Production software baseline for N. benthamiana; public reference overrides remain disabled.
Other packaged codon-reference assets are retained for provenance, reproducibility, and controlled internal sensitivity analysis only. They are not shown as public product choices, and public API/UI reference overrides remain unsupported.
Sequence Design Profile
FactorForge Default
Pre-synthesis safety baseline. Enforces 5′ initiation ramp (nt 1–45 low-GC clamp), homopolymer veto (≤5 nt), and standard Type IIS avoidance.
Choose options in the form, then save current settings. The example download is a starting template. Uploading YAML/JSON applies its mode, design settings and review levels to this screen and saves them in this browser. It does not run a calculation or approve a laboratory SOP. For 3DP, upload the structure and review positions again.
🛡️
Protein Conservation
100% Identity Preserved
⚙️
Design Constraints
Standard Stretch Limits
📋
Review Policy
Advisory / Action Thresholds
⚠️
Example configuration · Not an approved laboratory SOP.
Preset Details & Type IIS Rules ▾
Enforces BsaI, BpiI, and BsmBI avoidance with 5′ initiation ramp GC clamp and homopolymer veto.
🧪 Experimental Comparisons (Unavailable) Arg/Ser · Splice · 5′ Boundary
These comparison controls are not connected to web execution. They remain disabled and do not change the generated CDS. Existing engine constraints and advisory checks are separate.
Balanced 50/50 Arg (AGA/AGG) & 5-way Ser 20% quota
Comparison unavailable; motif findings are advisory, not confirmed splicing
Comparison unavailable; no reference-CDS boundary lock is applied by this control
Manual overrides (advanced)
Sequence & assembly requirements
Use the same integer to reproduce optimizer candidate selection.
Type IIS Enzymes to Avoid
Selected presets are merged with custom sites and removed by synonymous substitution where possible.
Sites will be removed from CDS by synonymous substitution where possible.
Review policy
Required failures produce FAIL; preferred warnings produce CONDITIONAL PASS.
Codon Allocation Policy
Balanced Non-CpGSynonymous codon distribution and methylation-risk avoidance.
🧬
Optimizing sequence...
📊 Design Review
🧬
Awaiting a sequence
Your design review will stay here throughout the workflow.
📊 Quality
CAI and GC review
📈 Candidates
Method comparison
🧾 Evidence
Reproducible report
🧬 Checks
Pre-synthesis review
⚙️
Active Configuration
Host: N. benthamiana · Profile: FactorForge Default · Standard Safety Baseline
FactorForge design principle
Same Protein. Transparently Redesigned DNA.
FactorForge redesigns synonymous codons and sequence-level features for the target plant host while strictly preserving the encoded amino-acid sequence.
Original DNA→Synonymous optimization→Exact translated protein
Synonymous shifts
N/ACDS reference requiredUnchanged
N/AExact codon matchesAA substitutions
N/ATranslation comparison unavailable
🚀
DESIGN CANDIDATE GENERATED
Review the computational checks before synthesis or experimental use.
Automated Decision
Unavailable
Sequence checks
Computational review| Metric | Original | Optimized |
|---|---|---|
| Sequence Length | - | - |
| GC Content | - | - |
| CAI Score | - | - |
| Codon Changes | N/A | - |
| AA Preserved | — | ✅ 100% |
GC Distribution (50bp Window) — ■ Reference Band
Calculated sequence comparison
1D Codon Optimization Map
5′ initiation ramp · nt 1–30
Original
Optimized
Rare <20%Low 20–35%Moderate 35–50%High 50–70%Very high >70%N/A
Codon position & amino acidHover over a track
Original → optimized—
Observed effects
Only measured effects are reported; optimizer causality is not inferred.
Hard constraint checks—
CAI Score
-
GC % Content
-
Target: —
PolyA Signals Found
-
Host Profile
-
Design Comparison & Decision Report
Rule vs ML Preview
Experimental · work in progress| Metric | Rule-Based | ML Preview | Delta / Status |
|---|
Codon Alignment
Reviewer Disposition
3D Structure & External Tools
NB-Fold 3D viewer runs directly inside your browser. AlphaFold DB / ESM Atlas open in external tabs.