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 Based on discusisons during the International Type III Secretion Meeting in Tübingen (Germany) in April 2016, a unified nomenclature for injectisome-type [[https://en.wikipedia.org/wiki/Type_three_secretion_system|type III secretion sytems]] was proposed in 2020 (Wagner & Diepold, 2020). This nomenclature was also advertised in the corresponding [[https://t3sswiki.science/w/index.php?title=Nomenclature_of_Type_III_Secretion_Systems|Wiki entry]]. At the same time, it was suggested to continue using the original name for T3SS chaperones and effectors. Algorithms to predict bacterial type III effectors are listed below. Based on discusisons during the International Type III Secretion Meeting in Tübingen (Germany) in April 2016, a unified nomenclature for injectisome-type [[https://en.wikipedia.org/wiki/Type_three_secretion_system|type III secretion sytems]] was proposed in 2020 (Wagner & Diepold, 2020). This nomenclature was also advertised in the corresponding [[https://t3sswiki.science/w/index.php?title=Nomenclature_of_Type_III_Secretion_Systems|Wiki entry]]. At the same time, it was suggested to continue using the original name for T3SS chaperones and effectors. Algorithms to predict bacterial type III effectors are listed below.
  
-^ Name                        ^ Purpose                                                                ^ URL                                                                                                                 ^ Reference                                               ^ +^Name ^Purpose ^URL ^Reference | 
-| Effectidor                  | T3E prediction                                                         | [[https://effectidor.tau.ac.il/|https://effectidor.tau.ac.il]]                                                      | Wagner //et al.//, 2022                                 | +|Effectidor |T3E prediction |[[https://effectidor.tau.ac.il/|https://effectidor.tau.ac.il]] |Wagner //et al.//, 2022a  | 
-| T3SEpp                      | T3E prediction                                                         | www.szu-bioinf.org/T3SEpp                                                                                           | Hui //et al.//, 2020                                    | +|Effectidor |T3E prediction |[[https://effectidor.tau.ac.il/|https://effectidor.tau.ac.il]] |Wagner //et al.//, 2022b  | 
-| ACNNT3                      | T3E prediction                                                         | Source code available at: [[https://github.com/Lijiesky/ACNNT3|https://github.com/Lijiesky/ACNNT3]]                 | Li //et al.//, 2020a                                    | +|DeepT3 2.0 |T3E prediction |[[http://advintbioinforlab.com/deept3/|http://advintbioinforlab.com/deept3/]] |Jing //et al.//, 2021  | 
-| EP3                         | T3E prediction                                                         | lab.malab.cn/~lijing/EP3.html                                                                                       | Li //et al.//, 2020b                                    | +|DeepT3_4 |T3E prediction |[[https://github.com/jingry/autoBioSeqpy/tree/2.0/examples/T3T4|github.com/jingry/autoBioSeqpy/tree/2.0/examples/T3T4]] |Yu //et al.//, 2021  | 
-| PrediTALE                   | TAL effector target prediction                                         | galaxy.informatik.uni-halle.de                                                                                      | Erkes //et al.//, 2019                                  | +|T3SEpp |T3E prediction |[[http://www.szu-bioinf.org/T3SEpp/|www.szu-bioinf.org/T3SEpp]] |Hui //et al.//, 2020  | 
-| Phylogenetic profiling      | T3E prediction                                                         | www.iib.unsam.edu.ar/orgsissec/                                                                                     | Zalguizuri //et al.//, 2019                             | +|ACNNT3 |T3E prediction |Source code available at: [[https://github.com/Lijiesky/ACNNT3|https://github.com/Lijiesky/ACNNT3]] |Li //et al.//, 2020a  | 
-| WEDeepT3                    | T3E prediction                                                         | [[https://bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html|bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html]]                       | Fu & Yang, 2019                                         | +|EP3 |T3E prediction |[[http://lab.malab.cn/~lijing/EP3.html|lab.malab.cn/~lijing/EP3.html]] |Li //et al.//, 2020b  | 
-| DeepT3                      | T3E prediction                                                         | [[https://github.com/lje00006/DeepT3|github.com/lje00006/DeepT3]]                                                   | Xue //et al.//, 2019                                    | +|PrediTALE |TAL effector target prediction |[[http://galaxy.informatik.uni-halle.de|galaxy.informatik.uni-halle.de]] |Erkes //et al.//, 2019  | 
-| Bastion3                    | T3E prediction                                                         | [[http://bastion3.erc.monash.edu/|bastion3.erc.monash.edu]]                                                         | Wang //et al.//, 2019                                   | +|Phylogenetic profiling |T3E prediction |[[http://www.iib.unsam.edu.ar/orgsissec/|www.iib.unsam.edu.ar/orgsissec/]] |Zalguizuri //et al.//, 2019  | 
-| Machine-learning algorithm  | T3E prediction                                                         |                                                                                                                     | Teper //et al.//, 2016                                  | +|WEDeepT3 |T3E prediction |[[https://bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html|bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html]] |Fu & Yang, 2019 | 
-| AnnoTALE                    | Annotation and analysis of TAL effector genes                          | www.jstacs.de/index.php/AnnoTALE                                                                                    | Grau //et al.//, 2016                                   | +|DeepT3 |T3E prediction |[[https://github.com/lje00006/DeepT3|github.com/lje00006/DeepT3]] |Xue //et al.//, 2019  | 
-| GenSET                      | T3E prediction                                                         |                                                                                                                     | Hobbs //et al.//, 2016                                  | +|Bastion3 |T3E prediction |[[http://bastion3.erc.monash.edu/|bastion3.erc.monash.edu]] |Wang //et al.//, 2019  | 
-| pEffect                     | T3E prediction                                                         | [[https://services.bromberglab.org/peffect/|services.bromberglab.org/peffect]]                                      | Goldberg //et al.//, 2016                               | +|Machine-learning algorithm |T3E prediction |  |Teper //et al.//, 2016  | 
-| QueTAL                      | Suite for the functional and phylogenetic comparison of TAL effectors  | bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi                                                                   | Pérez-Quintero //et al.//, 2015                         | +|AnnoTALE |Annotation and analysis of TAL effector genes |[[http://www.jstacs.de/index.php/AnnoTALE|www.jstacs.de/index.php/AnnoTALE]] |Grau //et al.//, 2016  | 
-| HMM-LDA                     | T3E prediction                                                         |                                                                                                                     | Yang & Qi, 2014                                         | +|GenSET |T3E prediction |  |Hobbs //et al.//, 2016  | 
-| Talvez                      | TAL effector target prediction                                         | bioinfo.mpl.ird.fr/cgi-bin/talvez/talvez.cgi                                                                        | Pérez-Quintero //et al.//, 2013                         | +|pEffect |T3E prediction |[[https://services.bromberglab.org/peffect/|services.bromberglab.org/peffect]] |Goldberg //et al.//, 2016  | 
-| TALgetter                   | TAL effector target prediction                                         | galaxy.informatik.uni-halle.de                                                                                      | Grau //et al.//, 2013                                   | +|QueTAL |Suite for the functional and phylogenetic comparison of TAL effectors |[[http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi|bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi]] |Pérez-Quintero //et al.//, 2015  | 
-| T3SPs                       | T3E prediction                                                         | cic.scu.edu.cn/bioinformatics/T3SPs.zip **(outdated)**                                                              | Yang //et al.//, 2013                                   | +|HMM-LDA |T3E prediction |  |Yang & Qi, 2014 | 
-| cSIEVE                      | T3E prediction                                                         |                                                                                                                     | Hovis //et al.//, 2013                                  | +|Talvez |TAL effector target prediction |[[http://bioinfo-web.mpl.ird.fr/cgi-bin2/talvez/talvez.cgi|bioinfo-web.mpl.ird.fr/cgi-bin2/talvez/talvez.cgi]] |Pérez-Quintero //et al.//, 2013  | 
-| T3_MM                       | T3E prediction                                                         | biocomputer.bio.cuhk.edu.hk/softwares/T3_MM (R package), biocomputer.bio.cuhk.edu.hk/T3DB/T3_MM.php **(outdated)**  | Wang //et al.//, 2013                                   | +|TALgetter |TAL effector target prediction |[[http://galaxy.informatik.uni-halle.de/|galaxy.informatik.uni-halle.de]] |Grau //et al.//, 2013  | 
-| BEAN                        | T3E prediction                                                         | systbio.cau.edu.cn/bean/                                                                                            | Dong //et al.//, 2013; Dong //et al.//, 2015            | +|T3SPs |T3E prediction |cic.scu.edu.cn/bioinformatics/T3SPs.zip **(outdated)**   |Yang //et al.//, 2013  | 
-| RalstoT3Edb                 | T3E prediction & database                                              | iant.toulouse.inra.fr/T3E                                                                                           | Peeters //et al.//, 2013; Sabbagh //et al.//, 2019      | +|cSIEVE |T3E prediction |  |Hovis //et al.//, 2013  | 
-| TALE-NT                     | TAL effector target prediction                                         | [[https://boglab.plp.iastate.edu|boglab.plp.iastate.edu]]                                                           | Doyle //et al.//, 2012                                  | +|T3_MM |T3E prediction |biocomputer.bio.cuhk.edu.hk/softwares/T3_MM (R package), biocomputer.bio.cuhk.edu.hk/T3DB/T3_MM.php **(outdated)**   |Wang //et al.//, 2013  | 
-| T3DB                        | T3E database                                                           | biocomputer.bio.cuhk.edu.hk/T3DB/ **(outdated)**                                                                    | Wang //et al.//, 2012                                   | +|BEAN |T3E prediction |[[http://systbio.cau.edu.cn/bean/|systbio.cau.edu.cn/bean/]] |Dong //et al.//, 2013; Dong //et al.//, 2015  | 
-| EffectPred                  | T3E prediction                                                         | Source code available at: www.p.chiba-u.ac.jp/lab/bisei/software/index.html **(outdated)**                          | Sato //et al.//, 2011                                   | +|RalstoT3Edb |T3E prediction & database |[[http://iant.toulouse.inra.fr/T3E|iant.toulouse.inra.fr/T3E]] |Peeters //et al.//, 2013; Sabbagh //et al.//, 2019  | 
-| BPBAac                      | T3E prediction                                                         | biocomputer.bio.cuhk.edu.hk/softwares/BPBAac/ **(outdated)**                                                        | Wang //et al.//, 2011                                   | +|TALE-NT |TAL effector target prediction |[[https://boglab.plp.iastate.edu|boglab.plp.iastate.edu]] |Doyle //et al.//, 2012  | 
-| HMM (EPIYA motif)           | T3E prediction                                                         |                                                                                                                     | Xu //et al.//, 2010                                     | +|T3DB |T3E database |biocomputer.bio.cuhk.edu.hk/T3DB/ **(outdated)**   |Wang //et al.//, 2012  | 
-| T3SEdb                      | T3E prediction & database                                              | effectors.bic.nus.edu.sg/T3SEdb/                                                                                    | Tay //et al.//, 2010                                    | +|EffectPred |T3E prediction |Source code available at: [[http://www.p.chiba-u.ac.jp/lab/bisei/software/index.html|www.p.chiba-u.ac.jp/lab/bisei/software/index.html]] **(outdated)**   |Sato //et al.//, 2011  | 
-| Classifier                  | T3E prediction                                                         | Discriminant functions available upon request                                                                       | Kampenusa & Zikmanis, 2010                              | +|BPBAac |T3E prediction |biocomputer.bio.cuhk.edu.hk/softwares/BPBAac/ **(outdated)**   |Wang //et al.//, 2011  | 
-| Classifier                  | T3E prediction                                                         | Method and data available upon request                                                                              | Yang //et al.//, 2010                                   | +|HMM (EPIYA motif) |T3E prediction |  |Xu //et al.//, 2010  | 
-| modlab                      | T3E prediction                                                         | gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html **(outdated)**                               | Löwer & Schneider, 2009                                 | +|T3SEdb |T3E prediction & database |effectors.bic.nus.edu.sg/T3SEdb/ **(outdated)**   |Tay //et al.//, 2010  | 
-| EffectiveT3                 | T3E prediction                                                         | www.effectors.org                                                                                                   | Arnold //et al.//, 2009                                 | +|Classifier |T3E prediction |Discriminant functions available upon request |Kampenusa & Zikmanis, 2010 | 
-| SIEVE                       | T3E prediction                                                         | www.sysbep.org/sieve/ **(outdated)**                                                                                | Samudrala //et al.//, 2009; McDermott //et al.//, 2011  |+|Classifier |T3E prediction |Method and data available upon request |Yang //et al.//, 2010  | 
 +|modlab |T3E prediction |gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html **(outdated)**   |Löwer & Schneider, 2009 | 
 +|EffectiveT3 |T3E prediction |[[http://www.effectors.org|www.effectors.org]] |Arnold //et al.//, 2009  | 
 +|SIEVE |T3E prediction |[[http://www.sysbep.org/sieve/|www.sysbep.org/sieve/]] **(outdated)**   |Samudrala //et al.//, 2009; McDermott //et al.//, 2011  | 
 +|//Pseudomonas//–Plant Interaction website  |T3E database |[[http://www.pseudomonas-syringae.org|www.pseudomonas-syringae.org]] |Lindeberg //et al.//, 2005  |
  
 ===== References ===== ===== References =====
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 Hui X, Chen Z, Lin M, Zhang J, Hu Y, Zeng Y, Cheng X, Ou-Yang L, Sun MA, White AP, Wang Y (2020). T3SEpp: an integrated prediction pipeline for bacterial type III secreted effectors. mSystems 5: e00288-20. DOI: [[https://doi.org/10.1128/mSystems|10.1128/mSystems]] Hui X, Chen Z, Lin M, Zhang J, Hu Y, Zeng Y, Cheng X, Ou-Yang L, Sun MA, White AP, Wang Y (2020). T3SEpp: an integrated prediction pipeline for bacterial type III secreted effectors. mSystems 5: e00288-20. DOI: [[https://doi.org/10.1128/mSystems|10.1128/mSystems]]
 +
 +Jing R, Wen T, Liao C, Xue L, Liu F, Yu L, Luo J (2021). DeepT3 2.0: improving type III secreted effector predictions by an integrative deep learning framework. NAR Genom. Bioinform. 3: lqab086. DOI[[https://doi.org/10.1093/nargab/lqab086|: 10.1093/nargab/lqab086]]
  
 Kampenusa I, Zikmanis P (2010). Distinguishable codon usage and amino acid composition patterns among substrates of leaderless secretory pathways from proteobacteria. Appl. Microbiol. Biotechnol. 86: 285-293. DOI: [[https://doi.org/10.1007/s00253-009-2423-8|10.1007/s00253-009-2423-8]] Kampenusa I, Zikmanis P (2010). Distinguishable codon usage and amino acid composition patterns among substrates of leaderless secretory pathways from proteobacteria. Appl. Microbiol. Biotechnol. 86: 285-293. DOI: [[https://doi.org/10.1007/s00253-009-2423-8|10.1007/s00253-009-2423-8]]
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 Li J, Wei L, Guo F, Zou Q (2020b). EP3: an ensemble predictor that accurately identifies type III secreted effectors. Brief. Bioinform., in press (bbaa008). DOI: [[https://doi.org/10.1093/bib/bbaa008|10.1093/bib/bbaa008]] Li J, Wei L, Guo F, Zou Q (2020b). EP3: an ensemble predictor that accurately identifies type III secreted effectors. Brief. Bioinform., in press (bbaa008). DOI: [[https://doi.org/10.1093/bib/bbaa008|10.1093/bib/bbaa008]]
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bacteria/t3e/software.1651937072.txt.gz · Last modified: 2023/01/09 10:20 (external edit)

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