ArticleMolecular biology and evolution2018
A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 35 citations in OpenAlex.
- Pooled it
- Systematic Detection of Alternative Open Reading Frames (altORFs) in Cancer Driver Genes.Journal of molecular evolution · 2026Article
- Next-Generation Vaccine Platforms: Integrating Synthetic Biology, Nanotechnology, and Systems Immunology for Improved Immunogenicity.Vaccines · 2025Review
- Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair.Journal of molecular evolution · 2023Article
- A novel ambigrammatic mycovirus, PsV5, works hand in glove with wheat stripe rust fungus to facilitate infection.Plant communications · 2023Article
- Identifying unique exposure-specific transgenerational differentially DNA methylated region epimutations in the genome using hybrid deep learning prediction models.Environmental epigenetics · 2023Article
- Article
- Computational methods for inferring location and genealogy of overlapping genes in virus genomes: approaches and applications.Current opinion in virology · 2022Review
- Article
- Persistence of Ambigrammatic Narnaviruses Requires Translation of the Reverse Open Reading Frame.Journal of virology · 2021Article
- Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution.Virology · 2021Article
- Review
- Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes.Frontiers in plant science · 2021Article
- Article
- Characterization of accessory genes in coronavirus genomes.Virology journal · 2020Article
- OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes.Molecular biology and evolution · 2020Article
- New insights into the evolutionary features of viral overlapping genes by discriminant analysis.Virology · 2020Article
- A case for a negative-strand coding sequence in a group of positive-sense RNA viruses.Virus evolution · 2020Article
- An exploration of ambigrammatic sequences in narnaviruses.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Overlapping genes in viruses maximize the coding capacity of their genomes and allow the generation of new genes without major increases in genome size. Despite their importance, the evolution and function of overlapping genes are often not well understood, in part due to difficulties in their detection. In addition, most bioinformatic approaches for the detection of overlapping genes require the comparison of multiple genome sequences that may not be available in metagenomic surveys of virus biodiversity. We introduce a simple new method for identifying candidate functional overlapping genes using single virus genome sequences. Our method uses randomization tests to estimate the expected length of open reading frames and then identifies overlapping open reading frames that significantly exceed this length and are thus predicted to be functional. We applied this method to 2548 reference RNA virus genomes and find that it has both high sensitivity and low false discovery for genes that overlap by at least 50 nucleotides. Notably, this analysis provided evidence for 29 previously undiscovered functional overlapping genes, some of which are coded in the antisense direction suggesting there are limitations in our current understanding of RNA virus replication.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.