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bacteria:t3e:software [2022/10/27 08:23]
rkoebnik 		bacteria:t3e:software [2022/10/27 15:26] (current)
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 ^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.//, 2022  |
 +|DeepT3 2.0 |T3E prediction |[[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  | |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  | |T3SEpp |T3E prediction |[[http://www.szu-bioinf.org/T3SEpp/|www.szu-bioinf.org/T3SEpp]] |Hui //et al.//, 2020  |
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 |EffectiveT3 |T3E prediction |[[http://www.effectors.org|www.effectors.org]] |Arnold //et al.//, 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 |SIEVE |T3E prediction |www.sysbep.org/sieve/ **(outdated)**   |Samudrala //et al.//, 2009; McDermott //et al.//, 2011  | |SIEVE |T3E prediction |www.sysbep.org/sieve/ **(outdated)**   |Samudrala //et al.//, 2009; McDermott //et al.//, 2011  |
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 ===== 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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