| name | mobileelementfinder |
| description | MobileElementFinder — CGE detection of named mobile genetic elements (MITEs, IS, Tn, ComTn, ICE, IME, CIME, …) in assembled bacterial genomes, with optional ARG/virulence context. Use for isolate mobilome screens. Upstream: PyPI MobileElementFinder / CGE web service. Route via cge-finders / microbial-mining; complement isescan, mobileog, integronfinder, genomad.
|
| license | MIT |
| category | analysis-tools |
| tags | ["MobileElementFinder","CGE","MGE","IS","transposon","ICE","IME","mobilome"] |
| upstream | https://pypi.org/project/MobileElementFinder/ |
| stage | mining |
MobileElementFinder
Upstream: MobileElementFinder (PyPI) ·
CGE service historically at genomicepidemiology.org · DB shipped with the tool
Citation
Johansson, M. H. K. et al. Detection of mobile genetic elements associated
with antibiotic resistance in Salmonella enterica using a newly developed web
tool: MobileElementFinder. J. Antimicrob. Chemother. 76, 101–109 (2021).
https://doi.org/10.1093/jac/dkaa390
See also docs/references.md and cge-finders.
Analytical thinking
MobileElementFinder aligns assemblies to a curated library of named MGEs
and can flag putative composite transposons. Complements:
| Tool | Role |
|---|
isescan | Broad IS HMM/annotation scan |
mobileog | MGE life-cycle protein families |
integronfinder | Integron architectures |
genomad | Plasmid/virus contig scores (meta) |
plasmidfinder | Replicon typing |
Hit ≠ proven mobilization event. Short-read assemblies under-resolve large ICE/IME.
How to run
MobileElementFinder -i assembly.fasta -o mef_out
Pin software + database versions from the installed package metadata.
Decision tree
Named MGE screen?
├─ CGE MGE library → mobileelementfinder
├─ IS-focused scan → isescan
├─ MGE protein machinery → mobileog
├─ Integrons → integronfinder
├─ Plasmid/virus contigs → genomad
└─ Replicons → plasmidfinder / mob-suite
Related skills
cge-finders · isescan · mobileog · integronfinder · plasmidfinder ·
genomad · resfinder · virulencefinder · microbial-mining ·
tool-selection
