Genome annotation basics: In DNA sequence analysis, what does the term “open reading frame (ORF)” most accurately refer to?

Introduction / Context:
Open reading frames (ORFs) are foundational to genome annotation. Identifying ORFs helps predict coding sequences before experimental validation. This concept appears in bioinformatics, molecular genetics, and biotechnology exams.

Given Data / Assumptions:

• We are dealing with raw or assembled DNA sequence.
• We want a definition that fits computational gene prediction.
• No organism restriction is implied.

Concept / Approach:

An ORF is a stretch of nucleotides that begins with a start codon (often ATG in DNA) and continues without encountering an in-frame stop codon (TAA, TAG, TGA) for a significant length, suggesting it could encode a polypeptide. ORFs are “putative genes” until confirmed by expression, conservation, or functional assays.

Step-by-Step Solution:

Verification / Alternative check:

Annotation pipelines combine ORF detection with ribosome binding site signals (prokaryotes), splice site models (eukaryotes), codon usage, and homology searches to refine gene calls, corroborating that ORFs are candidate coding sequences rather than confirmed genes.

Why Other Options Are Wrong:

• Bacteriophage sequence: too specific; ORFs exist in all genomes.
• Complete genome sequence: far broader than the ORF concept.
• Plasmid vector: a tool, not a definition of an ORF.

Common Pitfalls:

• Equating every ORF with a functional gene; some ORFs are false positives.
• Ignoring strand and frame; ORFs are frame-dependent.

Final Answer:

A possible gene predicted by DNA sequencing (a continuous stretch without in-frame stops)