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 ====== Software, Databases and Websites ====== ====== Software, Databases and Websites ======
  
-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/index.php/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 II |T3E prediction |[[https://effectidor.tau.ac.il/|https://effectidor.tau.ac.il]] |Wagner //et al.//, 2025  | 
-| T3SEpp                      | T3E prediction                                                         | www.szu-bioinf.org/T3SEpp                                                                                           | Hui //et al.//, 2020                                    | +|PLM-T3SE |T3E prediction |  |Gao //et al.//, 2025  | 
-| ACNNT3                      | T3E prediction                                                         | Source code available at: [[https://github.com/Lijiesky/ACNNT3|https://github.com/Lijiesky/ACNNT3]]                 | Li //et al.//, 2020a                                    | +|Effectidor |T3E prediction |[[https://effectidor.tau.ac.il/|https://effectidor.tau.ac.il]] |Wagner //et al.//, 2022a  | 
-| EP3                         | T3E prediction                                                         | lab.malab.cn/~lijing/EP3.html                                                                                       | Li //et al.//, 2020b                                    | +|Effectidor |T3E prediction |[[https://effectidor.tau.ac.il/|https://effectidor.tau.ac.il]] |Wagner //et al.//, 2022b  | 
-| PrediTALE                   | TAL effector target prediction                                         | galaxy.informatik.uni-halle.de                                                                                      | Erkes //et al.//, 2019                                  | +|DeepT3 2.0 |T3E prediction |[[http://advintbioinforlab.com/deept3/|http://advintbioinforlab.com/deept3/]] |Jing //et al.//, 2021  | 
-| Phylogenetic profiling      | T3E prediction                                                         | www.iib.unsam.edu.ar/orgsissec/                                                                                     | Zalguizuri //et al.//, 2019                             | +|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  | 
-| WEDeepT3                    | T3E prediction                                                         | [[https://bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html|bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html]]                       | Fu & Yang, 2019                                         | +|T3SEpp |T3E prediction |[[http://www.szu-bioinf.org/T3SEpp/|www.szu-bioinf.org/T3SEpp]] |Hui //et al.//, 2020  | 
-| DeepT3                      | T3E prediction                                                         | [[https://github.com/lje00006/DeepT3|github.com/lje00006/DeepT3]]                                                   | Xue //et al.//, 2019                                    | +|ACNNT3 |T3E prediction |Source code available at: [[https://github.com/Lijiesky/ACNNT3|https://github.com/Lijiesky/ACNNT3]] |Li //et al.//, 2020a  | 
-| Bastion3                    | T3E prediction                                                         | [[http://bastion3.erc.monash.edu/|bastion3.erc.monash.edu]]                                                         | Wang //et al.//, 2019                                   | +|EP3 |T3E prediction |[[http://lab.malab.cn/~lijing/EP3.html|lab.malab.cn/~lijing/EP3.html]] |Li //et al.//, 2020b  | 
-| Machine-learning algorithm  | T3E prediction                                                         |                                                                                                                     | Teper //et al.//, 2016                                  | +|PrediTALE |TAL effector target prediction |[[http://galaxy.informatik.uni-halle.de|galaxy.informatik.uni-halle.de]] |Erkes //et al.//, 2019  | 
-| AnnoTALE                    | Annotation and analysis of TAL effector genes                          | www.jstacs.de/index.php/AnnoTALE                                                                                    | Grau //et al.//, 2016                                   | +|Phylogenetic profiling |T3E prediction |[[http://www.iib.unsam.edu.ar/orgsissec/|www.iib.unsam.edu.ar/orgsissec/]] |Zalguizuri //et al.//, 2019  | 
-| GenSET                      | T3E prediction                                                         |                                                                                                                     | Hobbs //et al.//, 2016                                  | +|WEDeepT3 |T3E prediction |[[https://bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html|bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html]] |Fu & Yang, 2019 | 
-| pEffect                     | T3E prediction                                                         | [[https://services.bromberglab.org/peffect/|services.bromberglab.org/peffect]]                                      | Goldberg //et al.//, 2016                               | +|DeepT3 |T3E prediction |[[https://github.com/lje00006/DeepT3|github.com/lje00006/DeepT3]] |Xue //et al.//, 2019  | 
-| 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                         | +|Bastion3 |T3E prediction |[[http://bastion3.erc.monash.edu/|bastion3.erc.monash.edu]] |Wang //et al.//, 2019  | 
-| HMM-LDA                     | T3E prediction                                                         |                                                                                                                     | Yang & Qi, 2014                                         | +|Machine-learning algorithm |T3E prediction |  |Teper //et al.//, 2016  | 
-| Talvez                      | TAL effector target prediction                                         | bioinfo.mpl.ird.fr/cgi-bin/talvez/talvez.cgi                                                                        | Pérez-Quintero //et al.//, 2013                         | +|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  | 
-| TALgetter                   | TAL effector target prediction                                         | galaxy.informatik.uni-halle.de                                                                                      | Grau //et al.//, 2013                                   | +|GenSET |T3E prediction |  |Hobbs //et al.//, 2016  | 
-| T3SPs                       | T3E prediction                                                         | cic.scu.edu.cn/bioinformatics/T3SPs.zip **(outdated)**                                                              | Yang //et al.//, 2013                                   | +|pEffect |T3E prediction |[[https://services.bromberglab.org/peffect/|services.bromberglab.org/peffect]] |Goldberg //et al.//, 2016  | 
-| cSIEVE                      | T3E prediction                                                         |                                                                                                                     | Hovis //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  | 
-| 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                                   | +|HMM-LDA |T3E prediction |  |Yang & Qi, 2014 | 
-| BEAN                        | T3E prediction                                                         | systbio.cau.edu.cn/bean/                                                                                            | Dong //et al.//, 2013; Dong //et al.//, 2015            | +|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  | 
-| RalstoT3Edb                 | T3E prediction & database                                              | iant.toulouse.inra.fr/T3E                                                                                           | Peeters //et al.//, 2013; Sabbagh //et al.//, 2019      | +|TALgetter |TAL effector target prediction |[[http://galaxy.informatik.uni-halle.de/|galaxy.informatik.uni-halle.de]] |Grau //et al.//, 2013  | 
-| TALE-NT                     | TAL effector target prediction                                         | [[https://boglab.plp.iastate.edu|boglab.plp.iastate.edu]]                                                           | Doyle //et al.//, 2012                                  | +|T3SPs |T3E prediction |cic.scu.edu.cn/bioinformatics/T3SPs.zip **(outdated)**   |Yang //et al.//, 2013  | 
-| T3DB                        | T3E database                                                           | biocomputer.bio.cuhk.edu.hk/T3DB/ **(outdated)**                                                                    | Wang //et al.//, 2012                                   | +|cSIEVE |T3E prediction |  |Hovis //et al.//, 2013  | 
-| EffectPred                  | T3E prediction                                                         | Source code available at: www.p.chiba-u.ac.jp/lab/bisei/software/index.html **(outdated)**                          | Sato //et al.//, 2011                                   | +|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  | 
-| BPBAac                      | T3E prediction                                                         | biocomputer.bio.cuhk.edu.hk/softwares/BPBAac/ **(outdated)**                                                        | Wang //et al.//, 2011                                   | +|BEAN |T3E prediction |[[http://systbio.cau.edu.cn/bean/|systbio.cau.edu.cn/bean/]] |Dong //et al.//, 2013; Dong //et al.//, 2015  | 
-| HMM (EPIYA motif)           | T3E prediction                                                         |                                                                                                                     | Xu //et al.//, 2010                                     | +|RalstoT3Edb |T3E prediction & database |[[http://iant.toulouse.inra.fr/T3E|iant.toulouse.inra.fr/T3E]] |Peeters //et al.//, 2013; Sabbagh //et al.//, 2019  | 
-| T3SEdb                      | T3E prediction & database                                              | effectors.bic.nus.edu.sg/T3SEdb/                                                                                    | Tay //et al.//, 2010                                    | +|TALE-NT |TAL effector target prediction |[[https://boglab.plp.iastate.edu|boglab.plp.iastate.edu]] |Doyle //et al.//, 2012  | 
-| Classifier                  | T3E prediction                                                         | Discriminant functions available upon request                                                                       | Kampenusa & Zikmanis, 2010                              | +|T3DB |T3E database |biocomputer.bio.cuhk.edu.hk/T3DB/ **(outdated)**   |Wang //et al.//, 2012  | 
-| Classifier                  | T3E prediction                                                         | Method and data available upon request                                                                              | Yang //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  | 
-| modlab                      | T3E prediction                                                         | gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html **(outdated)**                               | Löwer & Schneider, 2009                                 | +|BPBAac |T3E prediction |biocomputer.bio.cuhk.edu.hk/softwares/BPBAac/ **(outdated)**   |Wang //et al.//, 2011  | 
-| EffectiveT3                 | T3E prediction                                                         | www.effectors.org                                                                                                   | Arnold //et al.//, 2009                                 | +|HMM (EPIYA motif) |T3E prediction |  |Xu //et al.//, 2010  | 
-| SIEVE                       | T3E prediction                                                         | www.sysbep.org/sieve/ **(outdated)**                                                                                | Samudrala //et al.//, 2009; McDermott //et al.//, 2011  |+|T3SEdb |T3E prediction & database |effectors.bic.nus.edu.sg/T3SEdb/ **(outdated)**   |Tay //et al.//, 2010  | 
 +|Classifier |T3E prediction |Discriminant functions available upon request |Kampenusa & Zikmanis, 2010 | 
 +|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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 Fu X, Yang Y (2019). WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning. Quant. Biol. 7: 293-301. DOI: [[https://doi.org/10.1007/s40484-019-0184-7|10.1007/s40484-019-0184-7]] Fu X, Yang Y (2019). WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning. Quant. Biol. 7: 293-301. DOI: [[https://doi.org/10.1007/s40484-019-0184-7|10.1007/s40484-019-0184-7]]
 +
 +Gao M, Song C, Liu T (2025). PLM-T3SE: Accurate prediction of type III secretion effectors using protein language model embeddings. J. Cell. Biochem. 126: e30642. DOI: [[https://doi.org/10.1002/jcb.30642|10.1002/jcb.30642]]
  
 Goldberg T, Rost B, Bromberg Y (2016). Computational prediction shines light on type III secretion origins. Sci. Rep. 6: 34516. DOI: [[https://doi.org/10.1038/srep34516|10.1038/srep34516]] Goldberg T, Rost B, Bromberg Y (2016). Computational prediction shines light on type III secretion origins. Sci. Rep. 6: 34516. DOI: [[https://doi.org/10.1038/srep34516|10.1038/srep34516]]
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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]]
  
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