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--- bacteria:t3e:software [2020/08/17 12:43] – [Table] rkoebnik
+++ bacteria:t3e:software [2023/09/11 17:32] (current) – [References] rkoebnik
@@ Line 1: / Line 1: @@
 ====== Software, Databases and Websites ======
-^ Name               ^ Purpose         ^ URL                                                                                                                                                                                                                             ^ Reference                                               ^
+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.
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-|                    |                 |                                                                                                                                                                                                                                 |                                                         |
-| T3SPs              | T3E prediction  | [[http://cic.scu.edu.cn/bioinformatics/T3SPs.zip|http://cic.scu.edu.cn/bioinformatics/T3SPs.zip]]                                                                                                                               | Yang //et al.//, 2013                                   |
-| cSIEVE             | T3E prediction  |                                                                                                                                                                                                                                 | Hovis //et al.//, 2013                                  |
-| T3_MM              | T3E prediction  | [[http://biocomputer.bio.cuhk.edu.hk/softwares/T3_MM|http://biocomputer.bio.cuhk.edu.hk/softwares/T3_MM]] (R package), [[http://biocomputer.bio.cuhk.edu.hk/T3DB/T3_MM.php|http://biocomputer.bio.cuhk.edu.hk/T3DB/T3_MM.php]]  | Wang //et al.//, 2013                                   |
-| BEAN               | T3E prediction  | protein.cau.edu.cn:8080/bean/ , [[http://systbio.cau.edu.cn/bean/|http://systbio.cau.edu.cn/bean/]]                                                                                                                             | Dong //et al.//, 2013; Dong //et al.//, 2015            |
-| EffectPred         | T3E prediction  | Source code for download (outdated): [[http://www.p.chiba-u.ac.jp/lab/bisei/software/index.html|http://www.p.chiba-u.ac.jp/lab/bisei/software/index.html]]                                                                      | Sato //et al.//, 2011                                   |
-| BPBAac             | T3E prediction  | http://biocomputer.bio.cuhk.edu.hk/softwares/BPBAac/ **(outdated)**                                                                                                                                                             | Wang //et al.//, 2011                                   |
-| HMM (EPIYA motif)  | T3E prediction  |                                                                                                                                                                                                                                 | Xu //et al.//, 2010                                     |
-| T3SEdb             | T3E prediction  | effectors.bic.nus.edu.sg/T3SEdb/                                                                                                                                                                                                | 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  | www.effectors.org                                                                                                                                                                                                               | Arnold //et al.//, 2009                                 |
-| SIEVE              | T3E prediction  | www.sysbep.org/sieve/ **(outdated)**                                                                                                                                                                                            | Samudrala //et al.//, 2009; McDermott //et al.//, 2011  |
-\\
+^Name ^Purpose ^URL ^Reference |
+|Effectidor |T3E prediction |[[https://effectidor.tau.ac.il/|https://effectidor.tau.ac.il]] |Wagner //et al.//, 2022a  |
+|Effectidor |T3E prediction |[[https://effectidor.tau.ac.il/|https://effectidor.tau.ac.il]] |Wagner //et al.//, 2022b  |
+|DeepT3 2.0 |T3E prediction |[[http://advintbioinforlab.com/deept3/|http://advintbioinforlab.com/deept3/]] |Jing //et al.//, 2021  |
+|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  |
+|T3SEpp |T3E prediction |[[http://www.szu-bioinf.org/T3SEpp/|www.szu-bioinf.org/T3SEpp]] |Hui //et al.//, 2020  |
+|ACNNT3 |T3E prediction |Source code available at: [[https://github.com/Lijiesky/ACNNT3|https://github.com/Lijiesky/ACNNT3]] |Li //et al.//, 2020a  |
+|EP3 |T3E prediction |[[http://lab.malab.cn/~lijing/EP3.html|lab.malab.cn/~lijing/EP3.html]] |Li //et al.//, 2020b  |
+|PrediTALE |TAL effector target prediction |[[http://galaxy.informatik.uni-halle.de|galaxy.informatik.uni-halle.de]] |Erkes //et al.//, 2019  |
+|Phylogenetic profiling |T3E prediction |[[http://www.iib.unsam.edu.ar/orgsissec/|www.iib.unsam.edu.ar/orgsissec/]] |Zalguizuri //et al.//, 2019  |
+|WEDeepT3 |T3E prediction |[[https://bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html|bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html]] |Fu & Yang, 2019 |
+|DeepT3 |T3E prediction |[[https://github.com/lje00006/DeepT3|github.com/lje00006/DeepT3]] |Xue //et al.//, 2019  |
+|Bastion3 |T3E prediction |[[http://bastion3.erc.monash.edu/|bastion3.erc.monash.edu]] |Wang //et al.//, 2019  |
+|Machine-learning algorithm |T3E prediction |  |Teper //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  |
+|GenSET |T3E prediction |  |Hobbs //et al.//, 2016  |
+|pEffect |T3E prediction |[[https://services.bromberglab.org/peffect/|services.bromberglab.org/peffect]] |Goldberg //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|bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi]] |Pérez-Quintero //et al.//, 2015  |
+|HMM-LDA |T3E prediction |  |Yang & Qi, 2014 |
+|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  |
+|TALgetter |TAL effector target prediction |[[http://galaxy.informatik.uni-halle.de/|galaxy.informatik.uni-halle.de]] |Grau //et al.//, 2013  |
+|T3SPs |T3E prediction |cic.scu.edu.cn/bioinformatics/T3SPs.zip **(outdated)**   |Yang //et al.//, 2013  |
+|cSIEVE |T3E prediction |  |Hovis //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  |
+|BEAN |T3E prediction |[[http://systbio.cau.edu.cn/bean/|systbio.cau.edu.cn/bean/]] |Dong //et al.//, 2013; Dong //et al.//, 2015  |
+|RalstoT3Edb |T3E prediction & database |[[http://iant.toulouse.inra.fr/T3E|iant.toulouse.inra.fr/T3E]] |Peeters //et al.//, 2013; Sabbagh //et al.//, 2019  |
+|TALE-NT |TAL effector target prediction |[[https://boglab.plp.iastate.edu|boglab.plp.iastate.edu]] |Doyle //et al.//, 2012  |
+|T3DB |T3E database |biocomputer.bio.cuhk.edu.hk/T3DB/ **(outdated)**   |Wang //et al.//, 2012  |
+|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  |
+|BPBAac |T3E prediction |biocomputer.bio.cuhk.edu.hk/softwares/BPBAac/ **(outdated)**   |Wang //et al.//, 2011  |
+|HMM (EPIYA motif) |T3E prediction |  |Xu //et al.//, 2010  |
+|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 =====
-McDermott JE, Corrigan A, Peterson E, Oehmen C, Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R, Heffron F (2011). Computational prediction of type III and IV secreted effectors in gram-negative bacteria. Infect. Immun. 79: 23-32. doi: [[https://doi.org/10.1128/IAI.00537-10|10.1128/IAI.00537-10]]
+Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S, Niinikoski A, Mewes HW, Horn M, Rattei T (2009). Sequence-based prediction of type III secreted proteins. PLoS Pathog. 5: e1000376. DOI: [[https://doi.org/10.1371/journal.ppat.1000376|10.1371/journal.ppat.1000376]]
-Samudrala R, Heffron F, McDermott JE (2009). Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. PLoS Pathog. 5: e1000375. doi: [[https://doi.org/10.1371/journal.ppat.1000375|10.1371/journal.ppat.1000375]]
+Dong X, Lu X, Zhang Z (2015). BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors. Database (Oxford) 2015: bav064. DOI: [[https://doi.org/10.1093/database/bav064|10.1093/database/bav064]]
-\\
+Dong X, Zhang YJ, Zhang Z. Using weakly conserved motifs hidden in secretion signals to identify type-III effectors from bacterial pathogen genomes. PLoS One. 2013;8(2):e56632. DOI: [[https://doi.org/10.1371/journal.pone.0056632|10.1371/journal.pone.0056632]]
+Doyle EL, Booher NJ, Standage DS, Voytas DF, Brendel VP, Vandyk JK, Bogdanove AJ (2012). TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res. 40: W117-W122. DOI: [[https://doi.org/10.1093/nar/gks608|10.1093/nar/gks608]]
+Erkes A, Mücke S, Reschke M, Boch J, Grau J (2019). PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting. PLoS Comput. Biol. 15: e1007206. DOI: [[https://doi.org/10.1371/journal.pcbi.1007206|10.1371/journal.pcbi.1007206]]
+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]]
+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]]
+Grau J, Reschke M, Erkes A, Streubel J, Morgan RD, Wilson GG, Koebnik R, Boch J (2016). AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from //Xanthomonas// genomic sequences. Sci. Rep. 6: 21077. DOI: [[https://doi.org/10.1038/srep21077|10.1038/srep21077]]
+Grau J, Wolf A, Reschke M, Bonas U, Posch S, Boch J (2013). Computational predictions provide insights into the biology of TAL effector target sites. PLoS Comput. Biol. 9: e1002962. DOI: [[https://doi.org/10.1371/journal.pcbi.1002962|10.1371/journal.pcbi.1002962]]
+Hobbs CK, Porter VL, Stow ML, Siame BA, Tsang HH, Leung KY (2016). Computational approach to predict species-specific type III secretion system (T3SS) effectors using single and multiple genomes. BMC Genomics 17: 1048. DOI: [[https://doi.org/10.1186/s12864-016-3363-1|10.1186/s12864-016-3363-1]]
+Hovis KM, Mojica S, McDermott JE, Pedersen L, Simhi C, Rank RG, Myers GS, Ravel J, Hsia RC, Bavoil PM @013). Genus-optimized strategy for the identification of chlamydial type III secretion substrates. Pathog. Dis. 69: 213-222. DOI: [[https://doi.org/10.1111/2049-632X.12070|10.1111/2049-632X.12070]]
+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]]
+Li J, Li Z, Luo J, Yao Y (2020a). ACNNT3: Attention-CNN framework for prediction of sequence-based bacterial type III secreted effectors. Comput. Math. Methods Med. 2020: 3974598. DOI: [[https://doi.org/10.1155/2020/3974598|10.1155/2020/3974598]]
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+===== Further Reading =====
+Noël LD, Denancé N, Szurek B (2013). Predicting promoters targeted by TAL effectors in plant genomes: from dream to reality. Front. Plant Sci. 4: 333. DOI: [[https://doi.org/10.3389/fpls.2013.00333|10.3389/fpls.2013.00333]]
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