Effectidor: an automated machine-learning based web server for the prediction of type-III secretion system effectors

Bioinformatics. 2022 Feb 14;btac087. doi: 10.1093/bioinformatics/btac087. Online ahead of print.

Abstract

Motivation: Type-III secretion systems are utilized by many Gram-negative bacteria to inject type 3 effectors (T3Es) to eukaryotic cells. These effectors manipulate host processes for the benefit of the bacteria and thus promote disease. They can also function as host-specificity determinants through their recognition as avirulence proteins that elicit immune response. Identifying the full effector repertoire within a set of bacterial genomes is of great importance to develop appropriate treatments against the associated pathogens.

Results: We present Effectidor, a user-friendly web server that harnesses several machine-learning techniques to predict T3Es within bacterial genomes. We compared the performance of Effectidor to other available tools for the same task on three pathogenic bacteria. Effectidor outperformed these tools in terms of classification accuracy (AUPRC above 0.98 in all cases).

Availability: Effectidor is available at: https://effectidor.tau.ac.il, and the source code is available at: https://github.com/naamawagner/Effectidor.

Supplementary information: Supplementary data are available at Bioinformatics online.