factorforge-cds 3.0.0__tar.gz → 3.1.0__tar.gz

{factorforge_cds-3.0.0 → factorforge_cds-3.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.0.0
+Version: 3.1.0
 Summary: FactorForge — open-source constraint-based CDS design engine by Eijex.
 Author-email: Eijex <eijex.lab@gmail.com>
 License:                                  Apache License
@@ -205,9 +205,9 @@ License:                                  Apache License
            See the License for the specific language governing permissions and
            limitations under the License.
         
-Project-URL: Homepage, https://factorforge.vercel.app
-Project-URL: Repository, https://github.com/eijex/factorforge
-Project-URL: Issues, https://github.com/eijex/factorforge/issues
+Project-URL: Homepage, https://factorforge-cds.vercel.app
+Project-URL: Repository, https://github.com/eijex/factorforge-cds
+Project-URL: Issues, https://github.com/eijex/factorforge-cds/issues
 Keywords: codon optimization,CDS design,synthetic biology,bioinformatics,Nicotiana benthamiana,constraint optimization,dynamic programming
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
@@ -219,6 +219,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: biopython>=1.81
 Requires-Dist: requests>=2.31
+Requires-Dist: click>=8.0
 Provides-Extra: ml
 Requires-Dist: torch>=2.0; extra == "ml"
 Requires-Dist: transformers>=4.35; extra == "ml"
@@ -227,6 +228,7 @@ Requires-Dist: pyyaml>=6.0; extra == "ml"
 Provides-Extra: dev
 Requires-Dist: pytest>=7.0; extra == "dev"
 Requires-Dist: ruff>=0.1; extra == "dev"
+Requires-Dist: pyyaml>=6.0; extra == "dev"
 Dynamic: license-file
 
 # FactorForge
@@ -235,8 +237,8 @@ Dynamic: license-file
 
 [![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](LICENSE)
 [![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-3.0.0-green.svg)](https://github.com/eijex/factorforge/releases)
-[![Web App](https://img.shields.io/badge/web-factorforge.vercel.app-brightgreen.svg)](https://factorforge.vercel.app)
+[![Version](https://img.shields.io/badge/version-3.1.0-green.svg)](https://github.com/eijex/factorforge-cds/releases)
+[![Web App](https://img.shields.io/badge/web-factorforge-cds.vercel.app-brightgreen.svg)](https://factorforge-cds.vercel.app)
 
 FactorForge optimizes protein sequences into *N. benthamiana*-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs.
 
@@ -266,8 +268,8 @@ print(result.metadata)   # CAI, GC%, scan results, domestication edits
 
 | Method | Description | Link |
 |--------|-------------|------|
-| **Web App** | No installation, demo & light use | [factorforge.vercel.app](https://factorforge.vercel.app) |
-| **CLI / Python** | Local use, batch processing, data privacy | `pip install factorforge` |
+| **Web App** | No installation, demo & light use | [factorforge-cds.vercel.app](https://factorforge-cds.vercel.app) |
+| **CLI / Python** | Local use, batch processing, data privacy | `pip install factorforge-cds` |
 | **Notebooks** | Training & experimentation on Colab / Kaggle | See [notebooks/](notebooks/) |
 
 ---
@@ -287,12 +289,17 @@ Protein sequence (FASTA or plain text)
         ▼
 2. Rule Scan
    Detects PolyA signals, homopolymers,
-   repeat sequences, forbidden restriction sites
+   CpG/TpA dinucleotide hotspots,
+   repeat sequences, rare codon runs,
+   forbidden restriction sites
         │
         ▼
 3. Domestication
    Removes Golden Gate / MoClo-incompatible
    BsaI / BsmBI recognition sites via silent edits
+   Optional custom restriction sites can be removed
+   by synonymous substitution when feasible
+   CpG/TpA reduction uses a CAI-budgeted balanced mode
         │
         ▼
 4. Output
@@ -343,20 +350,74 @@ Benchmarked on *N. benthamiana* codon usage table (v2 engine, 3,876 sequences):
 pip install factorforge-cds
 ```
 
-For ML features (ESM2 + BART decoder, experimental):
+Experimental ML research modules are available separately:
 
 ```bash
 pip install "factorforge-cds[ml]"
 ```
 
+> These modules (ESM2 + BART decoder) are not part of the stable v3.1.0 default optimizer.
+> The default v3.1.0 engine is the constraint-based DP feasibility engine.
+
 For development:
 
 ```bash
-git clone https://github.com/eijex/factorforge.git
+git clone https://github.com/eijex/factorforge-cds.git
 cd factorforge
 pip install -e ".[dev]"
 ```
 
+### Docker (local web app)
+
+Run the full web interface locally — no data leaves your machine:
+
+```bash
+docker pull ghcr.io/eijex/factorforge-cds:latest
+docker run -p 8080:8080 ghcr.io/eijex/factorforge-cds:latest
+```
+
+Then open [http://localhost:8080](http://localhost:8080).
+
+Or build from source:
+
+```bash
+git clone https://github.com/eijex/factorforge-cds.git
+cd factorforge
+docker build -t factorforge-cds .
+docker run -p 8080:8080 factorforge-cds
+```
+
+### Updating
+
+**PyPI (pip install):**
+
+```bash
+pip install --upgrade factorforge-cds
+```
+
+**Docker:**
+
+```bash
+docker pull ghcr.io/eijex/factorforge-cds:latest
+```
+
+**Git clone / local development:**
+
+```bash
+git pull origin main
+pip install -e ".[dev]"
+```
+
+To check your installed version:
+
+```bash
+pip show factorforge-cds
+# or
+factorforge --version
+```
+
+Release notes for each version are in [CHANGELOG.md](CHANGELOG.md).
+
 ---
 
 ## CLI Reference
@@ -399,8 +460,8 @@ Each optimized sequence includes:
 - **Optimized CDS** — synonymous codon replacements only, AA identity 100%
 - **CAI score** — codon adaptation index for *N. benthamiana*
 - **GC content** — global and first-region
-- **Scan report** — PolyA signals detected/fixed, homopolymers, restriction sites
-- **Domestication report** — BsaI/BsmBI sites removed, edit count
+- **Scan report** — PolyA signals detected/fixed, CpG/TpA hotspots, homopolymers, rare codon runs, restriction sites
+- **Domestication report** — BsaI/BsmBI and optional custom restriction sites removed, edit count
 - **Construct ID** — reproducible hash for tracking
 
 ---
@@ -417,7 +478,7 @@ FactorForge in your experiments, we'd love to hear from you:
 - How did CAI / GC% correlate with actual expression levels?
 - Any unexpected results?
 
-**Share your results** → [GitHub Issues](https://github.com/eijex/factorforge/issues)
+**Share your results** → [GitHub Issues](https://github.com/eijex/factorforge-cds/issues)
 or email: eijex.lab@gmail.com
 
 Validated results will be credited in [VALIDATION.md](VALIDATION.md) and future releases.
@@ -432,8 +493,8 @@ This project was built using the following tools and platforms:
 |------|------|
 | [Claude](https://claude.ai) / [Claude Code](https://claude.ai/code) (Anthropic) | Architecture design, domain analysis, code review |
 | [Codex](https://github.com/openai/codex) (OpenAI) | Code generation and implementation |
-| [Google Colab](https://colab.research.google.com) | ML training (Run 1, Run 2) |
-| [Kaggle](https://www.kaggle.com) | ML training (alpha_run1, alpha_run2) |
+| [Google Colab](https://colab.research.google.com) | ML training experiments |
+| [Kaggle](https://www.kaggle.com) | ML training experiments |
 | [ESM2](https://github.com/facebookresearch/esm) (Meta) | Protein language model (encoder) |
 | [PyTorch](https://pytorch.org) | ML framework |
 | [Conda](https://docs.conda.io) / [Miniconda](https://docs.anaconda.com/miniconda/) | Environment management |
@@ -449,8 +510,8 @@ This project was built using the following tools and platforms:
 If you use FactorForge in your research, please cite:
 
 ```
-FactorForge v3.0.0 (2026). Open-source constraint-based CDS design engine.
-Eijex. https://github.com/eijex/factorforge
+FactorForge v3.1.0 (2026). Open-source constraint-based CDS design engine.
+Eijex. https://github.com/eijex/factorforge-cds
 ```
 
 *A citable publication is in preparation. Until then, please cite the GitHub repository.*
@@ -470,6 +531,6 @@ own discretion.
 
 ## Get in Touch
 
-- **GitHub Issues** — bug reports, feature requests, wet-lab results: [github.com/eijex/factorforge/issues](https://github.com/eijex/factorforge/issues)
+- **GitHub Issues** — bug reports, feature requests, wet-lab results: [github.com/eijex/factorforge-cds/issues](https://github.com/eijex/factorforge-cds/issues)
 - **Email** — collaborations, feedback, questions: eijex.lab@gmail.com
-- **Web** — [factorforge.vercel.app](https://factorforge.vercel.app)
+- **Web** — [factorforge-cds.vercel.app](https://factorforge-cds.vercel.app)

{factorforge_cds-3.0.0 → factorforge_cds-3.1.0}/README.md

@@ -4,8 +4,8 @@
 
 [![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](LICENSE)
 [![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-3.0.0-green.svg)](https://github.com/eijex/factorforge/releases)
-[![Web App](https://img.shields.io/badge/web-factorforge.vercel.app-brightgreen.svg)](https://factorforge.vercel.app)
+[![Version](https://img.shields.io/badge/version-3.1.0-green.svg)](https://github.com/eijex/factorforge-cds/releases)
+[![Web App](https://img.shields.io/badge/web-factorforge-cds.vercel.app-brightgreen.svg)](https://factorforge-cds.vercel.app)
 
 FactorForge optimizes protein sequences into *N. benthamiana*-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs.
 
@@ -35,8 +35,8 @@ print(result.metadata)   # CAI, GC%, scan results, domestication edits
 
 | Method | Description | Link |
 |--------|-------------|------|
-| **Web App** | No installation, demo & light use | [factorforge.vercel.app](https://factorforge.vercel.app) |
-| **CLI / Python** | Local use, batch processing, data privacy | `pip install factorforge` |
+| **Web App** | No installation, demo & light use | [factorforge-cds.vercel.app](https://factorforge-cds.vercel.app) |
+| **CLI / Python** | Local use, batch processing, data privacy | `pip install factorforge-cds` |
 | **Notebooks** | Training & experimentation on Colab / Kaggle | See [notebooks/](notebooks/) |
 
 ---
@@ -56,12 +56,17 @@ Protein sequence (FASTA or plain text)
         ▼
 2. Rule Scan
    Detects PolyA signals, homopolymers,
-   repeat sequences, forbidden restriction sites
+   CpG/TpA dinucleotide hotspots,
+   repeat sequences, rare codon runs,
+   forbidden restriction sites
         │
         ▼
 3. Domestication
    Removes Golden Gate / MoClo-incompatible
    BsaI / BsmBI recognition sites via silent edits
+   Optional custom restriction sites can be removed
+   by synonymous substitution when feasible
+   CpG/TpA reduction uses a CAI-budgeted balanced mode
         │
         ▼
 4. Output
@@ -112,20 +117,74 @@ Benchmarked on *N. benthamiana* codon usage table (v2 engine, 3,876 sequences):
 pip install factorforge-cds
 ```
 
-For ML features (ESM2 + BART decoder, experimental):
+Experimental ML research modules are available separately:
 
 ```bash
 pip install "factorforge-cds[ml]"
 ```
 
+> These modules (ESM2 + BART decoder) are not part of the stable v3.1.0 default optimizer.
+> The default v3.1.0 engine is the constraint-based DP feasibility engine.
+
 For development:
 
 ```bash
-git clone https://github.com/eijex/factorforge.git
+git clone https://github.com/eijex/factorforge-cds.git
 cd factorforge
 pip install -e ".[dev]"
 ```
 
+### Docker (local web app)
+
+Run the full web interface locally — no data leaves your machine:
+
+```bash
+docker pull ghcr.io/eijex/factorforge-cds:latest
+docker run -p 8080:8080 ghcr.io/eijex/factorforge-cds:latest
+```
+
+Then open [http://localhost:8080](http://localhost:8080).
+
+Or build from source:
+
+```bash
+git clone https://github.com/eijex/factorforge-cds.git
+cd factorforge
+docker build -t factorforge-cds .
+docker run -p 8080:8080 factorforge-cds
+```
+
+### Updating
+
+**PyPI (pip install):**
+
+```bash
+pip install --upgrade factorforge-cds
+```
+
+**Docker:**
+
+```bash
+docker pull ghcr.io/eijex/factorforge-cds:latest
+```
+
+**Git clone / local development:**
+
+```bash
+git pull origin main
+pip install -e ".[dev]"
+```
+
+To check your installed version:
+
+```bash
+pip show factorforge-cds
+# or
+factorforge --version
+```
+
+Release notes for each version are in [CHANGELOG.md](CHANGELOG.md).
+
 ---
 
 ## CLI Reference
@@ -168,8 +227,8 @@ Each optimized sequence includes:
 - **Optimized CDS** — synonymous codon replacements only, AA identity 100%
 - **CAI score** — codon adaptation index for *N. benthamiana*
 - **GC content** — global and first-region
-- **Scan report** — PolyA signals detected/fixed, homopolymers, restriction sites
-- **Domestication report** — BsaI/BsmBI sites removed, edit count
+- **Scan report** — PolyA signals detected/fixed, CpG/TpA hotspots, homopolymers, rare codon runs, restriction sites
+- **Domestication report** — BsaI/BsmBI and optional custom restriction sites removed, edit count
 - **Construct ID** — reproducible hash for tracking
 
 ---
@@ -186,7 +245,7 @@ FactorForge in your experiments, we'd love to hear from you:
 - How did CAI / GC% correlate with actual expression levels?
 - Any unexpected results?
 
-**Share your results** → [GitHub Issues](https://github.com/eijex/factorforge/issues)
+**Share your results** → [GitHub Issues](https://github.com/eijex/factorforge-cds/issues)
 or email: eijex.lab@gmail.com
 
 Validated results will be credited in [VALIDATION.md](VALIDATION.md) and future releases.
@@ -201,8 +260,8 @@ This project was built using the following tools and platforms:
 |------|------|
 | [Claude](https://claude.ai) / [Claude Code](https://claude.ai/code) (Anthropic) | Architecture design, domain analysis, code review |
 | [Codex](https://github.com/openai/codex) (OpenAI) | Code generation and implementation |
-| [Google Colab](https://colab.research.google.com) | ML training (Run 1, Run 2) |
-| [Kaggle](https://www.kaggle.com) | ML training (alpha_run1, alpha_run2) |
+| [Google Colab](https://colab.research.google.com) | ML training experiments |
+| [Kaggle](https://www.kaggle.com) | ML training experiments |
 | [ESM2](https://github.com/facebookresearch/esm) (Meta) | Protein language model (encoder) |
 | [PyTorch](https://pytorch.org) | ML framework |
 | [Conda](https://docs.conda.io) / [Miniconda](https://docs.anaconda.com/miniconda/) | Environment management |
@@ -218,8 +277,8 @@ This project was built using the following tools and platforms:
 If you use FactorForge in your research, please cite:
 
 ```
-FactorForge v3.0.0 (2026). Open-source constraint-based CDS design engine.
-Eijex. https://github.com/eijex/factorforge
+FactorForge v3.1.0 (2026). Open-source constraint-based CDS design engine.
+Eijex. https://github.com/eijex/factorforge-cds
 ```
 
 *A citable publication is in preparation. Until then, please cite the GitHub repository.*
@@ -239,6 +298,6 @@ own discretion.
 
 ## Get in Touch
 
-- **GitHub Issues** — bug reports, feature requests, wet-lab results: [github.com/eijex/factorforge/issues](https://github.com/eijex/factorforge/issues)
+- **GitHub Issues** — bug reports, feature requests, wet-lab results: [github.com/eijex/factorforge-cds/issues](https://github.com/eijex/factorforge-cds/issues)
 - **Email** — collaborations, feedback, questions: eijex.lab@gmail.com
-- **Web** — [factorforge.vercel.app](https://factorforge.vercel.app)
+- **Web** — [factorforge-cds.vercel.app](https://factorforge-cds.vercel.app)

{factorforge_cds-3.0.0 → factorforge_cds-3.1.0}/pyproject.toml

@@ -1,52 +1,54 @@
-[build-system]
-requires = ["setuptools>=68", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "factorforge-cds"
-version = "3.0.0"
-description = "FactorForge — open-source constraint-based CDS design engine by Eijex."
-readme = "README.md"
-license = { file = "LICENSE" }
-requires-python = ">=3.10"
-authors = [{ name = "Eijex", email = "eijex.lab@gmail.com" }]
-keywords = ["codon optimization", "CDS design", "synthetic biology", "bioinformatics", "Nicotiana benthamiana", "constraint optimization", "dynamic programming"]
-classifiers = [
-    "Development Status :: 4 - Beta",
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Python :: 3",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-]
-
-dependencies = [
-    "biopython>=1.81",
-    "requests>=2.31",
-]
-
-[project.optional-dependencies]
-ml = [
-    "torch>=2.0",
-    "transformers>=4.35",
-    "fair-esm>=2.0",
-    "pyyaml>=6.0",
-]
-dev = [
-    "pytest>=7.0",
-    "ruff>=0.1",
-]
-
-[project.urls]
-Homepage = "https://factorforge.vercel.app"
-Repository = "https://github.com/eijex/factorforge"
-Issues = "https://github.com/eijex/factorforge/issues"
-
-[project.scripts]
-factorforge = "factorforge.cli.main:main"
-
-[tool.setuptools.packages.find]
-where = ["src"]
-
-[tool.ruff]
-line-length = 100
-target-version = "py310"
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "factorforge-cds"
+version = "3.1.0"
+description = "FactorForge — open-source constraint-based CDS design engine by Eijex."
+readme = "README.md"
+license = { file = "LICENSE" }
+requires-python = ">=3.10"
+authors = [{ name = "Eijex", email = "eijex.lab@gmail.com" }]
+keywords = ["codon optimization", "CDS design", "synthetic biology", "bioinformatics", "Nicotiana benthamiana", "constraint optimization", "dynamic programming"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+    "biopython>=1.81",
+    "requests>=2.31",
+    "click>=8.0",
+]
+
+[project.optional-dependencies]
+ml = [
+    "torch>=2.0",
+    "transformers>=4.35",
+    "fair-esm>=2.0",
+    "pyyaml>=6.0",
+]
+dev = [
+    "pytest>=7.0",
+    "ruff>=0.1",
+    "pyyaml>=6.0",
+]
+
+[project.urls]
+Homepage = "https://factorforge-cds.vercel.app"
+Repository = "https://github.com/eijex/factorforge-cds"
+Issues = "https://github.com/eijex/factorforge-cds/issues"
+
+[project.scripts]
+factorforge = "factorforge.cli.main:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py310"

{factorforge_cds-3.0.0 → factorforge_cds-3.1.0}/src/factorforge/__init__.py

@@ -1,12 +1,11 @@
 """
 FactorForge - Codon Optimization Platform
 
-v1_archived: Rule-based v1 (Archived)
-v2: Rule-based (Production) — engine version 3.0.0
-v3: ML engine / v3-alpha (ESM2 + BART, in development)
+v2: Rule-based engine (Production)
+v3: ML engine (ESM2 + BART)
 """
 
-__version__ = "3.0.0"
+__version__ = "3.1.0"
 __author__ = "Eijex"
 
 # Auto-register engines (safe when running from source tree)

{factorforge_cds-3.0.0 → factorforge_cds-3.1.0}/src/factorforge/cli/main.py

@@ -113,8 +113,8 @@ def list_engines():
     type=click.Choice(["feasibility_best", "gc_target", "high_cai"], case_sensitive=False),
     help="DP objective",
 )
-@click.option("--gc-min", type=float, default=40.0, help="Minimum target GC percentage")
-@click.option("--gc-max", type=float, default=55.0, help="Maximum target GC percentage")
+@click.option("--gc-min", type=float, default=55.0, help="Minimum target GC percentage")
+@click.option("--gc-max", type=float, default=65.0, help="Maximum target GC percentage")
 @click.option("--template", "construct_template", help="Construct template name")
 @click.option("--output", "-o", help="Output file")
 @click.option("--format", "output_format", default="fasta", help="Output format (fasta, genbank)")

{factorforge_cds-3.0.0 → factorforge_cds-3.1.0}/src/factorforge/engines/__init__.py

@@ -29,7 +29,7 @@ def register_builtin_engines() -> None:
         "v2",
         RuleBasedOptimizer,
         metadata={
-            "version": "3.0.0",
+            "version": "3.1.0",
             "engine_type": "rule_based",
             "role": "legacy_fallback",
             "stable": True,

{factorforge_cds-3.0.0 → factorforge_cds-3.1.0}/src/factorforge/engines/v2/__init__.py

@@ -5,7 +5,7 @@ Production system (2026)
 Plant-specific rule-based optimization
 """
 
-__version__ = "3.0.0"
+__version__ = "3.1.0"
 
 from .optimizer import RuleBasedOptimizer
 from .pipeline import OptimizationPipeline

{factorforge_cds-3.0.0 → factorforge_cds-3.1.0}/src/factorforge/engines/v2/optimizer.py

@@ -17,7 +17,7 @@ class RuleBasedOptimizer(OptimizerEngine):
     """Rule-based optimization engine"""
 
     name = "Rule-based"
-    version = "3.0.0"
+    version = "3.1.0"
 
     def __init__(self) -> None:
         self.validator = InputValidator()

{factorforge_cds-3.0.0 → factorforge_cds-3.1.0}/src/factorforge/engines/v2/pipeline.py

@@ -199,6 +199,27 @@ class OptimizationPipeline:
                     f"Remaining: {polya_fix.get('remaining_violations', '?')}"
                 )
 
+        # Dinucleotide reduction pass (CpG/TpA greedy synonymous fix)
+        if self.rule_engine.scan_dinucleotides(optimized_dna):
+            dinu_fix = self.rule_engine.fix_dinucleotides(optimized_dna, mode="balanced")
+            if dinu_fix["success"]:
+                optimized_dna = dinu_fix["modified_seq"]
+                candidate_metrics["cai"] = round(self.translator.calculate_cai(optimized_dna), 4)
+                candidate_metrics["gc"] = self.translator.calculate_gc_content(optimized_dna)
+                candidate_metrics["score"] = calculate_composite_score(
+                    cai=candidate_metrics["cai"],
+                    gc=candidate_metrics["gc"],
+                    sequence=optimized_dna,
+                    profile=effective_profile,
+                )
+                logger.info(
+                    f"Dinucleotide reduction [{dinu_fix['mode']}]: "
+                    f"{dinu_fix['initial_count']} -> "
+                    f"{dinu_fix['final_count']} ({dinu_fix['reduction_pct']}% reduction, "
+                    f"CAI {dinu_fix['cai_before']} -> {dinu_fix['cai_after']}, "
+                    f"{dinu_fix['rounds']} round(s))"
+                )
+
         logger.debug("Scanning for final rule violations")
         scan_mode = str(kwargs.get("scan_mode", "full"))
         scan_include = kwargs.get("scan_include")

{factorforge_cds-3.0.0 → factorforge_cds-3.1.0}/src/factorforge/engines/v2/rules/reverse_translator.py

@@ -370,10 +370,10 @@ class ReverseTranslator:
         Balanced profile: CAI first, GC balanced
 
         - Preferred codon ratio: 70%
-        - Target GC: 45-55%
+        - Target GC: 55-65% (benchmark analysis 004: avg output 60.1%)
         """
-        target_gc_min = kwargs.get("target_gc_min", 45)
-        target_gc_max = kwargs.get("target_gc_max", 55)
+        target_gc_min = kwargs.get("target_gc_min", 55)
+        target_gc_max = kwargs.get("target_gc_max", 65)
         preferred_ratio = kwargs.get("preferred_ratio", 0.7)
         max_attempts = kwargs.get("max_gc_attempts", 10)
         if max_attempts < 1: