construct-generator

name	construct-generator
description	Generate expected plasmid maps by combining vector backbones with insert sequences. Use when the user asks about in-silico cloning, simulating cloning reactions, generating construct maps, or verifying clone sequences against expected products.
allowed-tools	Bash(construct_generator:*)

Construct Generator

Generate expected plasmid maps by combining vector backbones with insert sequences. Essential for clone verification workflows.

CLI Location

./construct_generator [flags]

What It Does

The construct generator creates in-silico plasmid maps representing the expected product of a cloning reaction. It:

1. Loads a vector backbone (from built-in library or local files)
2. Fetches an insert sequence (from NCBI or local file)
3. Simulates the cloning reaction based on method (LIC, Gibson, SLIC, restriction)
4. Outputs a GenBank file with proper annotations

Usage

List Available Vectors

./construct_generator -list-vectors

Shows all vectors from:

• Built-in defaults (438 series, common expression vectors)
• ~/.benchaid/vectors.yaml (user-defined)
• vectors/*.yaml (project-specific)

Generate a Construct

From NCBI accession:

./construct_generator \
  -vector 438-A \
  -insert-accession NM_007192 \
  -output my_construct.gb

From local file:

./construct_generator \
  -vector 438-A \
  -insert-file insert.fasta \
  -gene-name MyProtein \
  -output my_construct.gb

Cloning Methods

Method	Flag	Description
LIC	-method lic	Ligation Independent Cloning (default)
Gibson	-method gibson	Gibson Assembly
SLIC	-method slic	Sequence and Ligation Independent Cloning
Restriction	-method restriction	Traditional restriction enzyme cloning

Key Flags

Flag	Description
-vector	Vector name (from library) or path to .gb/.yaml file
-insert-accession	NCBI accession (NM_, NP_, XP_ prefixes)
-insert-file	Local FASTA/GenBank file for insert
-gene-name	Gene name for annotations (auto-detected from accession)
-output	Output GenBank file path
-method	Cloning method: lic, gibson, slic, restriction
-json	Also output JSON metadata
-validate	Run validation checks (frame, stop codons)
-list-vectors	List all available vectors

Vector Library

Built-in 438 Series

The 438 series vectors are bacterial expression vectors with various fusion tags:

Vector	Tag	Notes
438-A	His6	N-terminal His tag
438-B	His6-MBP	Maltose binding protein fusion
438-C	His6-GST	Glutathione S-transferase fusion
438-D	His6-Trx	Thioredoxin fusion
438-E	His6-NusA	NusA fusion for solubility
438-F	His6-SUMO	SUMO fusion with protease site
438-G	His6-GB1	GB1 domain fusion
438-H	His6-Halo	HaloTag fusion

Local Vectors

GenBank files in ./vectors/ are automatically available:

• vectors/438-A.gb through vectors/438-H.gb

Adding Custom Vectors

Create a YAML file in vectors/ or ~/.benchaid/vectors.yaml:

vectors:
  my-vector:
    file: path/to/vector.gb
    insert_site: 1234  # Position for insert
    method: lic        # Default cloning method
    description: "My custom expression vector"

Validation

When -validate is enabled, the tool checks:

1. Frame check: Insert is in-frame with vector ORF
2. Internal stops: No premature stop codons in the fusion
3. Insert length: Reasonable size for expression

Output Format

The output GenBank file includes:

• Full plasmid sequence with insert
• Annotated features:
  • Vector backbone elements
  • Insert CDS with gene name
  • Fusion tags
  • Promoters, terminators, origins
• Metadata in COMMENT section

Example Workflows

Standard Cloning Project

# 1. Design primers for the insert
./primer_cli.py --accession NM_007192 --index 1

# 2. Generate expected construct
./construct_generator \
  -vector 438-B \
  -insert-accession NM_007192 \
  -output expected_construct.gb

# 3. After cloning and sequencing, verify with orf_verifier
python3 scripts/orf_verifier_cli.py \
  --plasmid expected_construct.gb \
  --protein MKHHHHHHMS...

Using Local Insert File

# Generate construct from synthesized gene
./construct_generator \
  -vector 438-A \
  -insert-file synthesized_gene.fasta \
  -gene-name DSIF \
  -method lic \
  -output dsif_construct.gb

Batch Processing

# Generate constructs for multiple accessions
for acc in NM_007192 NM_001234 NM_005678; do
  ./construct_generator \
    -vector 438-B \
    -insert-accession $acc \
    -output constructs/${acc}.gb
done

Integration with Other Tools

Tool	Integration
primer_cli.py	Design primers for the same accession
orf_verifier_cli.py	Verify clones against expected construct
snapgene_cli.py	Convert SnapGene vectors to GenBank format
notion_cli.py	Download vectors from Notion database

Troubleshooting

"Vector not found"

• Run -list-vectors to see available vectors
• Check that vector files exist in vectors/ directory
• Ensure GenBank files have proper LOCUS line

"Could not fetch accession"

• Verify the accession exists at NCBI
• Check internet connectivity
• Use -insert-file with a local file instead

"Frame validation failed"

• The insert may not be in-frame with vector
• Check primer design includes correct reading frame
• Use -validate=false to skip validation if intentional