Restriction Digest Simulator

A command-line tool to simulate restriction enzyme digests of DNA sequences. Given a DNA sequence and a list of restriction enzymes, it predicts the resulting fragments, their lengths, and overhang types. Supports linear and circular sequences.

Features

• Supports common restriction enzymes (EcoRI, BamHI, HindIII, etc.)
• Handles palindromic and non-palindromic recognition sites
• Linear and circular sequence modes
• Outputs a table with fragment positions, lengths, and overhang types (5' overhang, 3' overhang, blunt)
• Reads DNA sequences directly or from FASTA files
• Lists available enzymes

Installation

git clone https://github.com/collinsamagorgerat/restriction-digest-simulator.git
cd restriction-digest-simulator

No external dependencies beyond Python 3.7+.

Usage

# Digest linear sequence
python -m restriction_digest -s "AAAGAATTCGGG" -e EcoRI

# Digest circular plasmid from FASTA
python -m restriction_digest -f plasmid.fasta -e EcoRI,BamHI --circular

# List available enzymes
python -m restriction_digest --list-enzymes

Example

$ python -m restriction_digest -s "AAAGAATTCGGG" -e EcoRI
   #  Start    End  Length Left Enzyme  Left Overhang  Right Enzyme Right Overhang
--------------------------------------------------------------------------------
   1      1      4       4 None         -              EcoRI        5' overhang   
   2      5     12       8 EcoRI        5' overhang    None         -             

License

MIT License. See LICENSE.