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T3SS_prediction specifications

Information


Unique identifier OMICS_19730
Name T3SS_prediction
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Stability No
Maintained No

Publication for T3SS_prediction

T3SS_prediction citations

 (8)
library_books

Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species

2017
PMCID: 5378436
PMID: 28381962
DOI: 10.5423/PPJ.OA.11.2016.0252

[…] SecretomeP server, which is used widely to predict secreted proteins, especially the NCSPs. with an S-score ≥ 0.5 (http://www.cbs.dtu.dk/services/SecretomeP/) (). In addition, the EffectiveT3 () and T3SS_prediction () servers were used to recognize potential type 3 effectors, which are NCSPs that are possibly secreted through the T3SS pathway, and are termed as type 3 non-classically secreted pro […]

library_books

Burkholderia pseudomallei type III secreted protein BipC: role in actin modulation and translocation activities required for the bacterial intracellular lifecycle

2016
PeerJ
PMCID: 5180589
PMID: 28028452
DOI: 10.7717/peerj.2532

[…] nment Search tool (BLAST) () and Protein Data Bank (PDB) (). Type three secretion effector (TTSE) translocation signal peptide online program, such as ModLab (http://gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html) (), T3SEdb (http://effectors.bic.nus.edu.sg/T3SEdb/predict.php) () and Effective T3 (http://www.effectors.org/index.jsp) () were used to predict the presence of T […]

library_books

Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus

2014
BMC Genomics
PMCID: 4320434
PMID: 25518728
DOI: 10.1186/1471-2164-15-1135

[…] rs could regulate T3SS genes to modulate bacterial virulence [], We analyzed sequences in this genomic island to determine whether there is any T3SS secreted protein. Using a combination of available T3SS prediction tools including T3_MM [], Effective T4 [], and T3SS effector prediction [], we found that the third protein in this genomic island showed positive results in all of the prediction tool […]

call_split

The Aeromonas salmonicida subsp. salmonicida exoproteome: determination of the complete repertoire of Type Three Secretion System effectors and identification of other virulence factors

2013
Proteome Sci
PMCID: 3852671
PMID: 24073886
DOI: 10.1186/1477-5956-11-42
call_split See protocol

[…] ttp://www.cbs.dtu.dk/services/SignalP/) [], TatP 1.0 server (http://www.cbs.dtu.dk/services/TatP/) [] and the T3SS effector prediction softwares from Modlab® (http://gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html) [] and EffectiveT3 (http://www.effectors.org/) []. The list of A. salmonicida ABC transporters was provided by ABCdb (https://www-abcdb.biotoul.fr/) [] and prohag […]

library_books

New players in the same old game: a system level in silico study to predict type III secretion system and effector proteins in bacterial genomes reveals common themes in T3SS mediated pathogenesis

2013
BMC Res Notes
PMCID: 3734048
PMID: 23890184
DOI: 10.1186/1756-0500-6-297

[…] SD and MA initiated the study. MA carried out the initial scripting for carrying out T3SS prediction. VS carried out the prediction of T3SS. SD carried out the effector analysis. SD and VS drafted and revised the manuscript. All authors approved the final version of the manuscript. […]

call_split

Clustering subspecies of Aeromonas salmonicida using IS630 typing

2013
BMC Microbiol
PMCID: 3608246
PMID: 23406017
DOI: 10.1186/1471-2180-13-36
call_split See protocol

[…] : 0.5% Optimization, 0% Band filtering, 0.5% Tolerance and ignore uncertain bands.Prediction of T3SS effectors was performed with the Modlab® online software (http://gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html) []. […]

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T3SS_prediction institution(s)
Johann Wolfgang Goethe-University, Chair for Chem- and Bioinformatics, Frankfurt, Germany
T3SS_prediction funding source(s)
Supported by the Centre for Membrane Proteomics and the Beilstein-Institut zur Forderung der Chemischen Wissenschaften.

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