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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
)
dnd
DB
: phosphorothioation of the DNA backbone.