ArticleNucleic acids research2007
Automated recognition of retroviral sequences in genomic data--RetroTector.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
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Who cites it
102 citing papers in PubMed.
- Activation of transposable elements is linked to a region- and cell type-specific interferon response in Parkinson's disease.Science advances · 2026Article
- HERVOminer: a sequence similarity-based approach for recognizing endogenous retrovirus origin of the peptidome.NPJ precision oncology · 2026Article
- A comprehensive annotation of conserved protein domains in human endogenous retroviruses.NAR genomics and bioinformatics · 2026Article
- Viviparity and beyond: captured endogenous retroviral envelope genes drive teleost physiological innovations.Molecular biology and evolution · 2026Article
- Retroviral insertions contributed to the divergence of human and chimpanzee brains.bioRxiv : the preprint server for biology · 2025Article
- Microglial deficiency in the ATRX chromatin remodeler elicits a viral mimicry immune response that impacts neuronal function and behavior.PLoS biology · 2025Article
- Crossing Wallace's line: an evolutionarily young gibbon ape leukemia virus like endogenous retrovirus identified from the Philippine flying lemur (Cynocephalus volans).Scientific reports · 2025Article
- A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals.Molecular biology and evolution · 2024Article
- Contrasting segregation patterns among endogenous retroviruses across the koala population.Communications biology · 2024Article
- Article
- Mechanistic regulation of HERV activation in tumors and implications for translational research in oncology.Frontiers in cellular and infection microbiology · 2024Review
- Endogenous retroviral solo-LTRs in human genome.Frontiers in genetics · 2024Review
- Comparison of Endogenous Alpharetroviruses (ALV-like) across Galliform Species: New Distant Proviruses.Microorganisms · 2023Article
- Unraveling the role of ZNF506 as a human PBS-pro-targeting protein for ERVP repression.Nucleic acids research · 2023Article
- The diverse evolutionary histories of domesticated metaviral capsid genes in mammals.bioRxiv : the preprint server for biology · 2023Article
- Endogenous Caulimovirids: Fossils, Zombies, and Living in Plant Genomes.Biomolecules · 2023Review
- Genome-wide identification of endogenous retrovirus elements and their active transcription in mink genome.mLife · 2023Article
- Long-term host-pathogen evolution of endogenous beta- and gammaretroviruses in mouse lemurs with little evidence of recent retroviral introgression.Virus evolution · 2023Article
- Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.Nature communications · 2022Article
42 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic genomes contain many endogenous retroviral sequences (ERVs). ERVs are often severely mutated, therefore difficult to detect. A platform independent (Java) program package, RetroTector (ReTe), was constructed. It has three basic modules: (i) detection of candidate long terminal repeats (LTRs), (ii) detection of chains of conserved retroviral motifs fulfilling distance constraints and (iii) attempted reconstruction of original retroviral protein sequences, combining alignment, codon statistics and properties of protein ends. Other features are prediction of additional open reading frames, automated database collection, graphical presentation and automatic classification. ReTe favors elements >1000-bp long due to its dependence on order of and distances between retroviral fragments. It detects single or low-copy-number elements. ReTe assigned a 'retroviral' score of 890-2827 to 10 exogenous retroviruses from seven genera, and accurately predicted their genes. In a simulated model, ReTe was robust against mutational decay. The human genome was analyzed in 1-2 days on a LINUX cluster. Retroviral sequences were detected in divergent vertebrate genomes. Most ReTe detected chains were coincident with Repeatmasker output and the HERVd database. ReTe did not report most of the evolutionary old HERV-L related and MalR sequences, and is not yet tailored for single LTR detection. Nevertheless, ReTe rationally detects and annotates many retroviral sequences.
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