ArticleBriefings in bioinformatics2024
Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Mapping the functional dark proteome in cancer.Nature reviews. Cancer · 2026Review
- A microprotein atlas of the human frontal cortex in Alzheimer's disease.Nature aging · 2026Article
- Deeply conserved and expressed small ORFs in the model beetle Tribolium castaneum.BMC biology · 2026Article
- Computational prediction-combined proteogenomics unveils widespread non-AUG translation initiation events in plants.Nucleic acids research · 2026Article
- Article
- Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms.Genome biology and evolution · 2026Article
- Ribosome Profiling for Novel Antigen Discovery.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- Proteogenomic Discovery of Novel Open Reading Frames With HLA Immune Presentation on Human β-Cells.Diabetes · 2025Article
- Emerging roles for microproteins as critical regulators of endoplasmic reticulum function and cellular homeostasis.Seminars in cell & developmental biology · 2025Review
- Eukaryotic Microproteins.Annual review of biochemistry · 2025Review
- Recent advances and perspectives on the development of circular RNA cancer vaccines.NPJ vaccines · 2025Review
- Deep learning to decode sites of RNA translation in normal and cancerous tissues.Nature communications · 2025Article
- Finding functional microproteins.Trends in genetics : TIG · 2025Review
- ShortStop: a machine learning framework for microprotein discovery.BMC methods · 2025Article
- Microprotein-encoding RNA regulation in cells treated with pro-inflammatory and pro-fibrotic stimuli.BMC genomics · 2024Article
- Small ORFs, Big Insights:Cells · 2024Review
- Rp3: Ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery.Nature communications · 2024Article
- Deep learning to decode sites of RNA translation in normal and cancerous tissues.bioRxiv : the preprint server for biology · 2024Article
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Abstract
Accurate and comprehensive annotation of microprotein-coding small open reading frames (smORFs) is critical to our understanding of normal physiology and disease. Empirical identification of translated smORFs is carried out primarily using ribosome profiling (Ribo-seq). While effective, published Ribo-seq datasets can vary drastically in quality and different analysis tools are frequently employed. Here, we examine the impact of these factors on identifying translated smORFs. We compared five commonly used software tools that assess open reading frame translation from Ribo-seq (RibORFv0.1, RibORFv1.0, RiboCode, ORFquant, and Ribo-TISH) and found surprisingly low agreement across all tools. Only ~2% of smORFs were called translated by all five tools, and ~15% by three or more tools when assessing the same high-resolution Ribo-seq dataset. For larger annotated genes, the same analysis showed ~74% agreement across all five tools. We also found that some tools are strongly biased against low-resolution Ribo-seq data, while others are more tolerant. Analyzing Ribo-seq coverage revealed that smORFs detected by more than one tool tend to have higher translation levels and higher fractions of in-frame reads, consistent with what was observed for annotated genes. Together these results support employing multiple tools to identify the most confident microprotein-coding smORFs and choosing the tools based on the quality of the dataset and the planned downstream characterization experiments of the predicted smORFs.
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