Microbial Bioinformatics Group at MML, SJTU

Database and tool:

DeepSecE: deep learning-based prediction of secreted proteins in Gram-negative bacteria.

ICEberg 3.0 and ICEfinder 2.0: bacterial integrative and conjugative elements. (ICEberg 2.0)

ICEO: a biological ontology for representing and analyzing bacterial integrative and conjugative elements.

KpVR: replicons, antibiotic resistance/virulence genes in K. pneumoniae plasmids.

oriTDB and oriTfinder: the origin sites of DNA transfer (oriT) in bacterial mobile genetic elements.

SecReT4: bacterial type IV secretion systems (T4SS).

T4SEfinder: predict type IV secreted effectors (T4SE).

SecReT6 v3.0: bacterial type VI secretion systems (T6SS).

ThioBase and ThioFinder: thiopeptides featured in genetics and chemistry.

TADB 3.0 and TAfinder 2.0: toxin-antitoxin loci in Bacteria and Archaea. (TADB 2.0)

VRprofile 2.0: detection of antibiotic resistance-associated mobilome in bacterial pathogens. (VRprofile 1.0)

dndDB: phosphorothioation of the DNA backbone.