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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.
  
-\\ +^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  | 
-| T3SEpp                      | T3E prediction                                                         | [[http://www.szu-bioinf.org/T3SEpp|www.szu-bioinf.org/T3SEpp]]                                                         | Hui //et al.//, 2020                                    | +|DeepT3 2.0 |T3E prediction |[[http://advintbioinforlab.com/deept3/]] |Jing //et al.//, 2021  | 
-| ACNNT3                      | T3E prediction                                                         | Source code available at: [[https://github.com/Lijiesky/ACNNT3|https://github.com/Lijiesky/ACNNT3]]                    | Li //et al.//, 2020a                                    | +|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  | 
-| EP3                         | T3E prediction                                                         | [[http://lab.malab.cn/~lijing/EP3.html|http://lab.malab.cn/~lijing/EP3.html]]                                          | Li //et al.//, 2020b                                    | +|T3SEpp |T3E prediction |[[http://www.szu-bioinf.org/T3SEpp/|www.szu-bioinf.org/T3SEpp]] |Hui //et al.//, 2020  | 
-| PrediTALE                   | TAL effector target prediction                                         | [[http://galaxy.informatik.uni-halle.de|http://galaxy.informatik.uni-halle.de]]                                        | Erkes //et al.//, 2019                                  | +|ACNNT3 |T3E prediction |Source code available at: [[https://github.com/Lijiesky/ACNNT3|https://github.com/Lijiesky/ACNNT3]] |Li //et al.//, 2020a  | 
-| Phylogenetic profiling      | T3E prediction                                                         | [[http://www.iib.unsam.edu.ar/orgsissec/|http://www.iib.unsam.edu.ar/orgsissec/]]                                      | Zalguizuri //et al.//, 2019                             | +|EP3 |T3E prediction |[[http://lab.malab.cn/~lijing/EP3.html|lab.malab.cn/~lijing/EP3.html]] |Li //et al.//, 2020b  | 
-| WEDeepT3                    | T3E prediction                                                         | [[https://bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html|https://bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html]]                  | Fu & Yang, 2019                                         | +|PrediTALE |TAL effector target prediction |[[http://galaxy.informatik.uni-halle.de|galaxy.informatik.uni-halle.de]] |Erkes //et al.//, 2019  | 
-| DeepT3                      | T3E prediction                                                         | [[https://github.com/lje00006/DeepT3|github.com/lje00006/DeepT3]]                                                      | Xue //et al.//, 2019                                    | +|Phylogenetic profiling |T3E prediction |[[http://www.iib.unsam.edu.ar/orgsissec/|www.iib.unsam.edu.ar/orgsissec/]] |Zalguizuri //et al.//, 2019  | 
-| Bastion3                    | T3E prediction                                                         | [[http://bastion3.erc.monash.edu/|bastion3.erc.monash.edu]]                                                            | Wang //et al.//, 2019                                   | +|WEDeepT3 |T3E prediction |[[https://bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html|bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html]] |Fu & Yang, 2019 | 
-| Machine-learning algorithm  | T3E prediction                                                         |                                                                                                                        | Teper //et al.//, 2016                                  | +|DeepT3 |T3E prediction |[[https://github.com/lje00006/DeepT3|github.com/lje00006/DeepT3]] |Xue //et al.//, 2019  | 
-| AnnoTALE                    | Annotation and analysis of TAL effector genes                          | [[http://www.jstacs.de/index.php/AnnoTALE|http://www.jstacs.de/index.php/AnnoTALE]]                                    | Grau //et al.//, 2016                                   | +|Bastion3 |T3E prediction |[[http://bastion3.erc.monash.edu/|bastion3.erc.monash.edu]] |Wang //et al.//, 2019  | 
-| GenSET                      | T3E prediction                                                         |                                                                                                                        | Hobbs //et al.//, 2016                                  | +|Machine-learning algorithm |T3E prediction |  |Teper //et al.//, 2016  | 
-| pEffect                     | T3E prediction                                                         | [[https://services.bromberglab.org/peffect/|services.bromberglab.org/peffect]]                                         | Goldberg //et al.//, 2016                               | +|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  | 
-| QueTAL                      | Suite for the functional and phylogenetic comparison of TAL effectors  | [[http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi|http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi]]  | Pérez-Quintero //et al.//, 2015                         | +|GenSET |T3E prediction |  |Hobbs //et al.//, 2016  | 
-| HMM-LDA                     | T3E prediction                                                         |                                                                                                                        | Yang & Qi, 2014                                         | +|pEffect |T3E prediction |[[https://services.bromberglab.org/peffect/|services.bromberglab.org/peffect]] |Goldberg //et al.//, 2016  | 
-| Talvez                      | TAL effector target prediction                                         | [[http://bioinfo.mpl.ird.fr/cgi-bin/talvez/talvez.cgi|http://bioinfo.mpl.ird.fr/cgi-bin/talvez/talvez.cgi]]            | Pérez-Quintero //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  | 
-| TALgetter                   | TAL effector target prediction                                         | galaxy.informatik.uni-halle.de                                                                                         | Grau //et al.//, 2013                                   | +|HMM-LDA |T3E prediction |  |Yang & Qi, 2014 | 
-| T3SPs                       | T3E prediction                                                         | cic.scu.edu.cn/bioinformatics/T3SPs.zip **(outdated)**                                                                 | Yang //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  | 
-| cSIEVE                      | T3E prediction                                                         |                                                                                                                        | Hovis //et al.//, 2013                                  | +|TALgetter |TAL effector target prediction |[[http://galaxy.informatik.uni-halle.de/|galaxy.informatik.uni-halle.de]] |Grau //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                                   | +|T3SPs |T3E prediction |cic.scu.edu.cn/bioinformatics/T3SPs.zip **(outdated)**   |Yang //et al.//, 2013  | 
-| BEAN                        | T3E prediction                                                         | systbio.cau.edu.cn/bean/                                                                                               | Dong //et al.//, 2013; Dong //et al.//, 2015            | +|cSIEVE |T3E prediction |  |Hovis //et al.//, 2013  | 
-| RalstoT3Edb                 | T3E prediction & database                                              | iant.toulouse.inra.fr/T3E                                                                                              | Peeters //et al.//, 2013; Sabbagh //et al.//, 2019      | +|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  | 
-| TALE-NT                     | TAL effector target prediction                                         | [[https://boglab.plp.iastate.edu|boglab.plp.iastate.edu]]                                                              | Doyle //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  | 
-| T3DB                        | T3E database                                                           | biocomputer.bio.cuhk.edu.hk/T3DB/ **(outdated)**                                                                       | Wang //et al.//, 2012                                   | +|RalstoT3Edb |T3E prediction & database |[[http://iant.toulouse.inra.fr/T3E|iant.toulouse.inra.fr/T3E]] |Peeters //et al.//, 2013; Sabbagh //et al.//, 2019  | 
-| EffectPred                  | T3E prediction                                                         | Source code available at: www.p.chiba-u.ac.jp/lab/bisei/software/index.html **(outdated)**                             | Sato //et al.//, 2011                                   | +|TALE-NT |TAL effector target prediction |[[https://boglab.plp.iastate.edu|boglab.plp.iastate.edu]] |Doyle //et al.//, 2012  | 
-| BPBAac                      | T3E prediction                                                         | biocomputer.bio.cuhk.edu.hk/softwares/BPBAac/ **(outdated)**                                                           | Wang //et al.//, 2011                                   | +|T3DB |T3E database |biocomputer.bio.cuhk.edu.hk/T3DB/ **(outdated)**   |Wang //et al.//, 2012  | 
-| HMM (EPIYA motif)           | T3E prediction                                                         |                                                                                                                        | Xu //et al.//, 2010                                     | +|EffectPred |T3E prediction |Source code available at: www.p.chiba-u.ac.jp/lab/bisei/software/index.html **(outdated)**   |Sato //et al.//, 2011  | 
-| T3SEdb                      | T3E prediction & database                                              | effectors.bic.nus.edu.sg/T3SEdb/                                                                                       | Tay //et al.//, 2010                                    | +|BPBAac |T3E prediction |biocomputer.bio.cuhk.edu.hk/softwares/BPBAac/ **(outdated)**   |Wang //et al.//, 2011  | 
-| Classifier                  | T3E prediction                                                         | Discriminant functions available upon request                                                                          | Kampenusa & Zikmanis, 2010                              | +|HMM (EPIYA motif) |T3E prediction |  |Xu //et al.//, 2010  | 
-| Classifier                  | T3E prediction                                                         | Method and data available upon request                                                                                 | Yang //et al.//, 2010                                   | +|T3SEdb |T3E prediction & database |effectors.bic.nus.edu.sg/T3SEdb/ **(outdated)**   |Tay //et al.//, 2010  | 
-| modlab                      | T3E prediction                                                         | gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html **(outdated)**                                  | Löwer & Schneider, 2009                                 | +|Classifier |T3E prediction |Discriminant functions available upon request |Kampenusa & Zikmanis, 2010 | 
-| EffectiveT3                 | T3E prediction                                                         | www.effectors.org                                                                                                      | Arnold //et al.//, 2009                                 | +|Classifier |T3E prediction |Method and data available upon request |Yang //et al.//, 2010  | 
-| SIEVE                       | T3E prediction                                                         | www.sysbep.org/sieve/ **(outdated)**                                                                                   | Samudrala //et al.//, 2009; McDermott //et al.//, 2011  |+|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 |www.sysbep.org/sieve/ **(outdated)**   |Samudrala //et al.//, 2009; McDermott //et al.//, 2011  |
  
 ===== 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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 Teper D, Burstein D, Salomon D, Gershovitz M, Pupko T, Sessa G (2016). Identification of novel //Xanthomonas euvesicatoria// type III effector proteins by a machine-learning approach. Mol. Plant Pathol. 17: 398-411. DOI: [[https://doi.org/10.1111/mpp.12288|10.1111/mpp.12288]] Teper D, Burstein D, Salomon D, Gershovitz M, Pupko T, Sessa G (2016). Identification of novel //Xanthomonas euvesicatoria// type III effector proteins by a machine-learning approach. Mol. Plant Pathol. 17: 398-411. DOI: [[https://doi.org/10.1111/mpp.12288|10.1111/mpp.12288]]
 +
 +Wagner N, Avram O, Gold-Binshtok D, Zerah B, Teper D, Pupko T (2022). Effectidor: an automated machine-learning based web server for the prediction of type-III secretion system effectors. Bioinformatics 38: 2341-2343. DOI: [[https://doi.org/10.1093/bioinformatics/btac087|10.1093/bioinformatics/btac087]]
 +
 +Wagner S, Diepold A (2020). A unified nomenclature for injectisome-type type III secretion systems. Curr. Top. Microbiol. Immunol. 427: 1-10. doi: [[https://doi.org/10.1007/82_2020_210|10.1007/82_2020_210]]
  
 Wang Y, Huang H, Sun M, Zhang Q, Guo D (2012). T3DB: an integrated database for bacterial type III secretion system. BMC Bioinformatics 13: 66. DOI: [[https://doi.org/10.1186/1471-2105-13-66|10.1186/1471-2105-13-66]] Wang Y, Huang H, Sun M, Zhang Q, Guo D (2012). T3DB: an integrated database for bacterial type III secretion system. BMC Bioinformatics 13: 66. DOI: [[https://doi.org/10.1186/1471-2105-13-66|10.1186/1471-2105-13-66]]
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 Yang Y, Zhao J, Morgan RL, Ma W, Jiang T (2010). Computational prediction of type III secreted proteins from gram-negative bacteria. BMC Bioinformatics 11: S47. DOI: [[https://doi.org/10.1186/1471-2105-11-S1-S47|10.1186/1471-2105-11-S1-S47]] Yang Y, Zhao J, Morgan RL, Ma W, Jiang T (2010). Computational prediction of type III secreted proteins from gram-negative bacteria. BMC Bioinformatics 11: S47. DOI: [[https://doi.org/10.1186/1471-2105-11-S1-S47|10.1186/1471-2105-11-S1-S47]]
 +
 +Yu L, Liu F, Li Y, Luo J, Jing R (2021). DeepT3_4: a hybrid deep neural network model for the distinction between bacterial type III and IV secreted effectors. Front. Microbiol. 12: 605782. DOI: [[https://doi.org/10.3389/fmicb.2021.605782|10.3389/fmicb.2021.605782]]
  
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