ORF Finder

Find open reading frames (ORFs) in DNA sequences.

Description

ORF Finder identifies all possible open reading frames in a given DNA sequence by scanning for start codons (ATG) and stop codons (TAA, TAG, TGA) across all six reading frames. It outputs the position, length, and translated protein sequence for each ORF found.

Installation

git clone https://github.com/wl5e/orf-finder.git
cd orf-finder
pip install -r requirements.txt

Usage

Basic usage

python orf_finder.py --sequence ATGAAATTTTAACCCGGG

From a FASTA file

python orf_finder.py --file input.fasta

Custom minimum ORF length

python orf_finder.py --file input.fasta --min-length 100

Output to file

python orf_finder.py --file input.fasta --output results.tsv

Output format

Tab-separated columns:

• Frame: reading frame (+1, +2, +3, -1, -2, -3)
• Start: start position (1-based)
• End: end position (1-based)
• Length: length in nucleotides
• Protein: translated amino acid sequence

Tests

pytest test_orf_finder.py -v

License

MIT