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T3S effector prediction software tools | Protein sequence analysis

T3SEs are proteins secreted by Gram-negative pathogenic bacteria to interfere with host immune signaling networks (Galan and Wolf-Watz, 2006; Galan, 2009). They are secreted into host cells through type-III secretion systems (T3SSs) (Galan and…
EffectiveDB
Dataset

EffectiveDB

Contains pre-calculated predictions of bacterial secreted proteins and of…

Contains pre-calculated predictions of bacterial secreted proteins and of intact secretion systems. EffectiveDB bundles various tools to recognize Type III secretion signals, conserved binding sites…

S4TE
Desktop

S4TE Searching algorithm for Type-IV secretion system Effectors

Permits in silico screening of proteobacteria genomes. S4TE predicts type IV…

Permits in silico screening of proteobacteria genomes. S4TE predicts type IV effectors (T4Es) based on the combined use of 13 distinctive features. It analyses the genome architecture and its hit…

SSE-ACC
Algorithm

SSE-ACC SSE amino acid composition

Permits to represent protein sequence features. SSE-ACC uses amino acid…

Permits to represent protein sequence features. SSE-ACC uses amino acid composition (AAC), k-mer composition, and amino acid composition methods to extract concerned features. It is able to generate…

BEAN
Web

BEAN Bacterial Effector Analyzer

An integrated web resource to predict, analyse and store type III secreted…

An integrated web resource to predict, analyse and store type III secreted effectors (T3SEs). BEAN 2.0 includes three major components. First, it provides an accurate T3SE predictor based on a hybrid…

RF T3SPs
Desktop

RF T3SPs Random Forest algorithm for Type III Secreted Proteins

Predicts novel Type III secretion systems (T3SPs) using position-specific…

Predicts novel Type III secretion systems (T3SPs) using position-specific residue conservation profiles. RF T3SPs is based on a random forests model. It gives a high receiver operating curve (AUC) of…

T346Hunter
Web

T346Hunter Type Three, Four and Six secretion system Hunter

A web-based tool for the identification and localisation of type III, type IV…

A web-based tool for the identification and localisation of type III, type IV and type VI secretion systems (T3SS, T4SS and T6SS, respectively) clusters in bacterial genomes. T346Hunter makes use of…

EffectiveT3
Desktop

EffectiveT3

A prediction software for type III effector proteins. EffectiveT3 is based on a…

A prediction software for type III effector proteins. EffectiveT3 is based on a machine learning approach and can be applied to single proteins as well as complete proteomes. The great value of the…

T4SEpre
Web

T4SEpre

An inter-species T4S effector prediction tool based on position-specific amino…

An inter-species T4S effector prediction tool based on position-specific amino acid composition features in C-termini. T4SEpre is used to predict new Type IV secretion system (T4SS) effectors from H.…

pEffect
Web

pEffect

Predicts type III effector proteins from protein sequence. pEffect combines…

Predicts type III effector proteins from protein sequence. pEffect combines sequence similarity-based inferences (PSI-BLAST) with de-novo predictions using machine learning techniques. It identifies…

T4EffPred
Web

T4EffPred

Predicts effector proteins secreted by Type IV secretion systems of…

Predicts effector proteins secreted by Type IV secretion systems of Gram-negative bacteria. T4EffPred was developed by computing four classes of sequence features such as amino acid composition,…

BPBAac
Desktop
Web

BPBAac

A T3S effector prediction tool based on position-specific amino acid…

A T3S effector prediction tool based on position-specific amino acid composition features in N-termini. BPBAac model outperformed other implementations in classification of T3S and non-T3S proteins,…

RF model
Desktop

RF model

A prediction model across 16 species was developed using random forest to…

A prediction model across 16 species was developed using random forest to classify T3SPs and non-T3 SPs, with high receiver operating curve of 0.93 in the 10-fold cross validation. Based on the…

T3SS effector…
Web

T3SS effector prediction

Predicts the existence of type III secretion system (T3SS) signals in amino…

Predicts the existence of type III secretion system (T3SS) signals in amino acid sequences. T3SS effector prediction is a machine learning approach to identify potential T3SS effectors by their…

T3_MM
Desktop
Web

T3_MM

Calculates the total amino acid composition (Aac) conditional probability…

Calculates the total amino acid composition (Aac) conditional probability difference, i.e., the likelihood ratio of a sequence being a T3S or a non-T3S protein. With T3_MM, known T3S and non-T3S…

T3SEdb
Web

T3SEdb

A specialized database of annotated T3SS effector (T3SE) sequences containing…

A specialized database of annotated T3SS effector (T3SE) sequences containing 1089 records from 46 bacterial species compiled from the literature and public protein databases. Procedures have been…

T3DB
Dataset

T3DB Type-III-Secretion-System related database

Aimed to annotate all bacterial T3SS related structure, effector, regulator,…

Aimed to annotate all bacterial T3SS related structure, effector, regulator, and auxiliary genes.

T3SEpre
Web

T3SEpre

Identification of new type III secreted proteins based on position-specific…

Identification of new type III secreted proteins based on position-specific sequence-structure joint features. T3SEpre is a highly effective T3S effector prediction model based on joint features…

T3SS_prediction
Web

T3SS_prediction

Identifies potential multi sub-unit type III secretion systems (T3SS) effectors…

Identifies potential multi sub-unit type III secretion systems (T3SS) effectors by their N-terminal amino acid sequence. T3SS_prediction uses a sliding window procedure in combination with artificial…

SIEVE Server
Web

SIEVE Server

A public web tool for prediction of type III secreted effectors. The SIEVE…

A public web tool for prediction of type III secreted effectors. The SIEVE Server scores potential secreted effectors from genomes of bacterial pathogens with type III secretion systems using a model…

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