ArticleBMC bioinformatics2006
Detecting overlapping coding sequences in virus genomes.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 1 of them a synthesis that pooled it.
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Who cites it
59 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Insight into the Biology of Hepatitis B Virus and Recent Therapeutic Approaches.Current microbiology · 2026Review
- Programmed ribosomal frameshifting duringScience advances · 2025Article
- A novel ilarvirus protein CP-RT is expressed via stop codon readthrough and suppresses RDR6-dependent RNA silencing.PLoS pathogens · 2024Article
- Synonymous nucleotide changes drive papillomavirus evolution.Tumour virus research · 2022Review
- Review
- Molecular Characterization of the Nsp2 and ORF5 (ORF5a) Genes of PRRSV Strains in Nine Provinces of China During 2016-2018.Frontiers in veterinary science · 2021Article
- OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes.Molecular biology and evolution · 2020Article
- Orientation-dependent toxic effect of human papillomavirus type 33 long control region DNA in Escherichia coli cells.Virus genes · 2020Article
- Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing.Scientific reports · 2019Article
- An upstream protein-coding region in enteroviruses modulates virus infection in gut epithelial cells.Nature microbiology · 2019Article
- A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences.Molecular biology and evolution · 2018Article
- Phage spanins: diversity, topological dynamics and gene convergence.BMC bioinformatics · 2018Article
- Transcriptional and Translational Landscape of Equine Torovirus.Journal of virology · 2018Article
- Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes.PloS one · 2018Article
- Mitochondrial dual-coding genes in Trypanosoma brucei.PLoS neglected tropical diseases · 2017Article
- Article
- Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes.BMC microbiology · 2017Article
- Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.Frontiers in microbiology · 2017Review
- Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.Nucleic acids research · 2016Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDetecting new coding sequences (CDSs) in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which can result in unusual patterns of codon usage; conservation between related sequences can be difficult to interpret--especially within overlapping genes; and viruses often employ non-canonical translational mechanisms--e.g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites--which can conceal potentially coding open reading frames (ORFs).
resultsIn a previous paper we introduced a new statistic--MLOGD (Maximum Likelihood Overlapping Gene Detector)--for detecting and analysing overlapping CDSs. Here we present (a) an improved MLOGD statistic, (b) a greatly extended suite of software using MLOGD, (c) a database of results for 640 virus sequence alignments, and (d) a web-interface to the software and database. Tests show that, from an alignment with just 20 mutations, MLOGD can discriminate non-overlapping CDSs from non-coding ORFs with a typical accuracy of up to 98%, and can detect CDSs overlapping known CDSs with a typical accuracy of 90%. In addition, the software produces a variety of statistics and graphics, useful for analysing an input multiple sequence alignment.
conclusionMLOGD is an easy-to-use tool for virus genome annotation, detecting new CDSs--in particular overlapping or short CDSs--and for analysing overlapping CDSs following frameshift sites. The software, web-server, database and supplementary material are available at http://guinevere.otago.ac.nz/mlogd.html.
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