{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T16:13:57Z","timestamp":1775664837813,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"24","funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Various human pathogens secret effector proteins into hosts cells via the type IV secretion system (T4SS). These proteins play important roles in the interaction between bacteria and hosts. Computational methods for T4SS effector prediction have been developed for screening experimental targets in several isolated bacterial species; however, widely applicable prediction approaches are still unavailable<\/jats:p>\n               <jats:p>Results: In this work, four types of distinctive features, namely, amino acid composition, dipeptide composition, .position-specific scoring matrix composition and auto covariance transformation of position-specific scoring matrix, were calculated from primary sequences. A classifier, T4EffPred, was developed using the support vector machine with these features and their different combinations for effector prediction. Various theoretical tests were performed in a newly established dataset, and the results were measured with four indexes. We demonstrated that T4EffPred can discriminate IVA and IVB effectors in benchmark datasets with positive rates of 76.7% and 89.7%, respectively. The overall accuracy of 95.9% shows that the present method is accurate for distinguishing the T4SS effector in unidentified sequences. A classifier ensemble was designed to synthesize all single classifiers. Notable performance improvement was observed using this ensemble system in benchmark tests. To demonstrate the model\u2019s application, a genome-scale prediction of effectors was performed in Bartonella henselae, an important zoonotic pathogen. A number of putative candidates were distinguished.<\/jats:p>\n               <jats:p>Availability: A web server implementing the prediction method and the source code are both available at http:\/\/bioinfo.tmmu.edu.cn\/T4EffPred.<\/jats:p>\n               <jats:p>Contact: \u00a0hoofuquan@yahoo.com.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt554","type":"journal-article","created":{"date-parts":[[2013,9,25]],"date-time":"2013-09-25T03:45:09Z","timestamp":1380080709000},"page":"3135-3142","source":"Crossref","is-referenced-by-count":106,"title":["Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles"],"prefix":"10.1093","volume":"29","author":[{"given":"Lingyun","family":"Zou","sequence":"first","affiliation":[{"name":"1 Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University (TMMU), Chongqing 40038, China and 2Department of Tuberculosis, Institute of Infectious TB Prevention, Third Hospital of PLA, Baoji, Shanxi 721006, China"}]},{"given":"Chonghan","family":"Nan","sequence":"additional","affiliation":[{"name":"1 Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University (TMMU), Chongqing 40038, China and 2Department of Tuberculosis, Institute of Infectious TB Prevention, Third Hospital of PLA, Baoji, Shanxi 721006, China"}]},{"given":"Fuquan","family":"Hu","sequence":"additional","affiliation":[{"name":"1 Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University (TMMU), Chongqing 40038, China and 2Department of Tuberculosis, Institute of Infectious TB Prevention, Third Hospital of PLA, Baoji, Shanxi 721006, China"}]}],"member":"286","published-online":{"date-parts":[[2013,9,23]]},"reference":[{"key":"2023012810484368300_btt554-B1","doi-asserted-by":"crossref","first-page":"e1000376","DOI":"10.1371\/journal.ppat.1000376","article-title":"Sequence-based prediction of type III secreted proteins","volume":"5","author":"Arnold","year":"2009","journal-title":"PLoS Pathog."},{"key":"2023012810484368300_btt554-B2","doi-asserted-by":"crossref","first-page":"D660","DOI":"10.1093\/nar\/gks1248","article-title":"SecReT4: a web-based bacterial type IV secretion system TF4resource","volume":"41","author":"Bi","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012810484368300_btt554-B3","doi-asserted-by":"crossref","first-page":"e1000508","DOI":"10.1371\/journal.ppat.1000508","article-title":"Genome-scale identification of Legionella pneumophila effectors using a machine learning approach","volume":"5","author":"Burstein","year":"2009","journal-title":"PLoS Pathog."},{"key":"2023012810484368300_btt554-B4","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1111\/j.1600-0854.2006.00446.x","article-title":"Recognition and delivery of effector proteins into eukaryotic cells by bacterial secretion systems","volume":"7","author":"Cambronne","year":"2006","journal-title":"Traffic"},{"key":"2023012810484368300_btt554-B5","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1038\/nature08588","article-title":"Structure of the outer membrane complex of a type IV secretion system","volume":"462","author":"Chandran","year":"2009","journal-title":"Nature"},{"key":"2023012810484368300_btt554-B6","doi-asserted-by":"crossref","first-page":"21755","DOI":"10.1073\/pnas.1010485107","article-title":"Large-scale identification and translocation of type IV secretion substrates by Coxiella burnetii","volume":"107","author":"Chen","year":"2010","journal-title":"Proc. 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