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Molecular Diagnosis and Diversity for Regulated Xanthomonas
Bacterial virulence factors
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| Name | Purpose | URL | Reference |
|---|---|---|---|
| T3SPs | T3E prediction | 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 (R package), 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/ | 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| EffectPred | T3E prediction | Source code for download (outdated): http://www.p.chiba-u.ac.jp/lab/bisei/software/index.html | Sato et al., 2011 |
| BPBAac | T3E prediction | http://biocomputer.bio.cuhk.edu.hk/softwares/BPBAac/ (outdated) | Wang et al., 2011 |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| modlab | T3E prediction | gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html (outdated) | Löwer & Schneider, 2009 |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| SIEVE | T3E prediction | www.sysbep.org/sieve/ (outdated) | Samudrala et al., 2009; McDermott et al., 2011 |
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: 10.1128/IAI.00537-10
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: 10.1371/journal.ppat.1000375
