ArticleBioinformatics (Oxford, England)2025
Effectidor II: a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Identification of protein secretion systems and type III effectors in wood-associated bacteria of the genusMicrobiology spectrum · 2026Article
- Pan-genome and antibiotic resistance insights into Xanthomonas citri pv. punicae pathotypes.BMC microbiology · 2026Article
- Machine learning for the prediction of gram-negative bacterial secreted effectors: advances and challenges.Frontiers in chemistry · 2026Review
- Novel insights into the genetic basis and transcriptomic elucidation of virulence attenuation inVirulence · 2025Article
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11 authors.
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Abstract
motivationType III secretion systems are used by many Gram-negative bacteria to inject type 3 effectors (T3Es) directly into eukaryotic cells, promoting disease or provoking immune response. Because of these opposing evolutionary forces, T3E repertoires often vary within taxonomic groups. Identifying the full effector gene repertoire in genomes of related individuals is crucial for determining core and specialized effectors, understanding the disease dynamics, and developing appropriate management strategies against pathogens. It can also help uncover novel T3Es that have recently emerged in a population. Our previously published Effectidor web server successfully addressed the challenge of identifying T3Es in a single bacterial genome. Here, we enriched the web server with various novel capabilities, including the identification of T3Es from multiple genome sequences simultaneously.
resultsWe present Effectidor II, a web server that relies on machine learning to predict T3E-encoding genes within bacterial pan-genomes. We demonstrate the benefit of learning based on features extracted from the entire sequences comprising the pan-genome and report a novel T3E discovered by it in Xanthomonas euroxanthea. AVAILABILITY AND IMPLEMENTATION: Effectidor II is available at: https://effectidor.tau.ac.il and the source code is available at: https://github.com/naamawagner/Effectidor. A stand-alone version of Effectidor II is available at: https://github.com/naamawagner/Effectidor/tree/StandAlone. The source code for the standalone version and the data used in this work are also provided in https://doi.org/10.5281/zenodo.15081636.
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