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Molecular Diagnosis and Diversity for Regulated Xanthomonas
Bacterial virulence factors
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| Name | Purpose | URL | Reference |
|---|---|---|---|
| GenSET | T3E prediction | Hobbs et al., 2016 | |
| pEffect | T3E prediction | services.bromberglab.org/peffect | Goldberg et al., 2016 |
| HMM-LDA | T3E prediction | Yang & Qi, 2014 | |
| T3SPs | T3E prediction | cic.scu.edu.cn/bioinformatics/T3SPs.zip (outdated) | Yang et al., 2013 |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| T3E prediction | biocomputer.bio.cuhk.edu.hk/softwares/T3_MM (R package), biocomputer.bio.cuhk.edu.hk/T3DB/T3_MM.php (outdated) | Wang et al., 2013 |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 | systbio.cau.edu.cn/bean/ | Dong et al., 2013; Dong et al., 2015 |
| EffectPred | T3E prediction | Source code for download: www.p.chiba-u.ac.jp/lab/bisei/software/index.html (outdated) | Sato et al., 2011 |
| BPBAac | T3E prediction | biocomputer.bio.cuhk.edu.hk/softwares/BPBAac/ (outdated) | Wang et al., 2011 |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 | 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| modlab | T3E prediction | gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html (outdated) | Löwer & Schneider, 2009 |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| SIEVE | T3E prediction | www.sysbep.org/sieve/ (outdated) | Samudrala et al., 2009; McDermott et al., 2011 |
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: 10.1371/journal.ppat.1000376
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: 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: 10.1371/journal.pone.0056632
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: 10.1111/2049-632X.12070
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: 10.1007/s00253-009-2423-8
Löwer M, Schneider G (2009). Prediction of type III secretion signals in genomes of gram-negative bacteria. PLoS One 4: e5917. doi: 10.1371/journal.pone.0005917. Erratum in: PLoS One (2009); 4. doi: 10.1371/annotation/78c8fc32-b1e2-4c87-9c92-d318af980b9b
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
Sato Y, Takaya A, Yamamoto T (2011). Meta-analytic approach to the accurate prediction of secreted virulence effectors in gram-negative bacteria. BMC Bioinformatics 12: 442. doi: 10.1186/1471-2105-12-442
Tay DM, Govindarajan KR, Khan AM, Ong TY, Samad HM, Soh WW, Tong M, Zhang F, Tan TW (2010). T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System. BMC Bioinformatics 11: S4. doi: 10.1186/1471-2105-11-S7-S4
Wang Y, Sun M, Bao H, White AP (2013). T3_MM: a Markov model effectively classifies bacterial type III secretion signals. PLoS One 8: e58173. doi: 10.1371/journal.pone.0058173
Wang Y, Zhang Q, Sun MA, Guo D (2011). High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles. Bioinformatics 27: 777-784. doi: 10.1093/bioinformatics/btr021
Xu S, Zhang C, Miao Y, Gao J, Xu D (2010). Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif. BMC Genomics 11: S1. doi: 10.1186/1471-2164-11-S3-S1
Yang X, Guo Y, Luo J, Pu X, Li M (2013). Effective identification of Gram-negative bacterial type III secreted effectors using position-specific residue conservation profiles. PLoS One 8: e84439. doi: 10.1371/journal.pone.0084439
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: 10.1186/1471-2105-11-S1-S47
