Open Reading Frames

Finding Genes

An Open Reading Frame (ORF) is a stretch of DNA that could encode a protein. It starts at an ATG start codon and ends at the first in-frame stop codon (TAA, TAG, or TGA).

...AAATGCGATAACC...
      ↑ start    ↑ stop
      ATG→CGA→TAA

To find an ORF:

1. Scan the sequence for ATG
2. From that ATG, read codons in triplets
3. Return the sequence from ATG up to and including the first stop codon

def find_orf(seq):
    for i in range(len(seq) - 2):
        if seq[i:i+3] == "ATG":
            for j in range(i, len(seq) - 2, 3):
                codon = seq[j:j+3]
                if codon in ("TAA", "TAG", "TGA"):
                    return seq[i:j+3]
    return ""

print(find_orf("AAATGCGATAA"))   # ATGCGATAA
print(find_orf("ATGTTTGCCTAG"))  # ATGTTTGCCTAG
print(find_orf("AAACCC"))        # (empty — no ORF)

AlphaGenome predicts where genes start and end across hundreds of different cell types — essentially running this kind of search at genomic scale with learned, cell-type-specific rules.

Your Task

Implement find_orf(seq) that returns the first ORF found, or an empty string if none exists.