open reading frame
Definition
An open reading frame (ORF) is a continuous stretch of DNA or RNA nucleotide codons that begins with a start codon (typically ATG) and ends with a stop codon (TAA, TAG, or TGA), potentially encoding a protein. ORFs represent candidate protein-coding sequences within genomes and transcripts. In genomics, identifying ORFs is crucial for gene prediction and annotation, as they indicate regions likely to be translated into functional proteins. ORFs can exist in any of the six possible reading frames (three on each DNA strand). The longest ORF in a sequence is often considered the most likely to encode a functional protein, though shorter ORFs may also produce bioactive peptides. ORF analysis is fundamental for understanding genome organization, discovering novel genes, and predicting proteomes across organisms.
Visualize open reading frame in Nodes Bio
Researchers can visualize networks connecting predicted ORFs to their encoded proteins, regulatory elements, and functional pathways. Nodes Bio enables mapping relationships between multiple ORFs in polycistronic transcripts, their translation products, and downstream protein-protein interactions. Users can integrate ORF predictions with expression data to identify which candidate sequences are actively translated, creating networks that link genomic features to phenotypic outcomes and revealing functional gene clusters.
Visualization Ideas:
- ORF-to-protein networks showing translation products and their functional annotations
- Genomic context networks displaying overlapping ORFs and their regulatory relationships
- Multi-omics integration networks connecting predicted ORFs with ribosome profiling and proteomics data
Example Use Case
A research team studying antibiotic resistance in bacteria discovers an unusual genomic region through whole-genome sequencing. They identify multiple overlapping ORFs within this locus, including several small ORFs previously annotated as non-coding. By analyzing ribosome profiling data, they confirm active translation of these small ORFs. Network analysis reveals that the encoded peptides interact with known resistance proteins, suggesting a novel multi-component resistance mechanism. This discovery leads to identifying new therapeutic targets for combating drug-resistant infections.