{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T08:35:42Z","timestamp":1770971742095,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T00:00:00Z","timestamp":1748304000000},"content-version":"vor","delay-in-days":28,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institutes of Food and Agriculture"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Type 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf272","type":"journal-article","created":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T19:29:40Z","timestamp":1745954980000},"source":"Crossref","is-referenced-by-count":5,"title":["Effectidor II: a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors"],"prefix":"10.1093","volume":"41","author":[{"given":"Naama","family":"Wagner","sequence":"first","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Chaim Levanon St 30 , Tel Aviv, 69978,","place":["Israel"]}]},{"given":"Ella","family":"Baumer","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Chaim Levanon St 30 , Tel Aviv, 69978,","place":["Israel"]}]},{"given":"Iris","family":"Lyubman","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Chaim Levanon St 30 , Tel Aviv, 69978,","place":["Israel"]}]},{"given":"Yair","family":"Shimony","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Chaim Levanon St 30 , Tel Aviv, 69978,","place":["Israel"]}]},{"given":"Noam","family":"Bracha","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Chaim Levanon St 30 , Tel Aviv, 69978,","place":["Israel"]}]},{"given":"Leonor","family":"Martins","sequence":"additional","affiliation":[{"name":"CIBIO\u2014Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO\u2014Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o, 4485-661,","place":["Portugal"]},{"name":"FCUP\u2014Faculdade de Ci\u00eancias, Departamento de Biologia, Universidade do Porto , Porto, 4169-007,","place":["Portugal"]}]},{"given":"Neha","family":"Potnis","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, Auburn University , Auburn, AL, 36849,","place":["United States of America"]}]},{"given":"Jeff H","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR, 97331,","place":["United States of America"]}]},{"given":"Doron","family":"Teper","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology and Weed Research, Institute of Plant Protection Agricultural Research Organization (ARO), Volcani Center , Rishon LeZion, 7505101,","place":["Israel"]}]},{"given":"Ralf","family":"Koebnik","sequence":"additional","affiliation":[{"name":"Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAe, Institut Agro, IRD , Montpellier, 34394,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9463-2575","authenticated-orcid":false,"given":"Tal","family":"Pupko","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. 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