ArticleComputational and structural biotechnology journal2024
EEfinder, a general purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes.
Article in Computational and structural biotechnology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Comparative Genomic Characterization of a Megaplasmid-harboring Multidrug-Resistant Raoultella ornithinolytica from a Septic Diabetic Patient in Uganda.Current microbiology · 2026Article
- HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements.Bioinformatics (Oxford, England) · 2025Article
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3 authors.
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Abstract
Horizontal gene transfer is a phenomenon of genetic material transmission between species with no parental relationship. It has been characterized among several major branches of life, including among prokaryotes, viruses and eukaryotes. The characterization of endogenous elements derived from viruses or bacteria provides a snapshot of past host-pathogen interactions and coevolution as well as reference information to remove false positive results from metagenomic studies. Currently there is a lack of general purpose standardized tools for endogenous elements screening which limits reproducibility and hinder comparative analysis between studies. Here we describe EEfinder, a new general purpose tool for identification and classification of endogenous elements derived from viruses or bacteria found in eukaryotic genomes. The tool was developed to include six common steps performed in this type of analysis: data cleaning, similarity search through sequence alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements and flanks extraction. We evaluated the sensitivity of EEfinder to identify endogenous elements through comparative analysis using data from the literature and showed that EEfinder automatically detected 97 % of the EVEs compared to published results obtained by manual curation and detected an almost exact full integration of a
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