mobileelementfinder

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

# pip install MobileElementFinder (or docker per upstream)
# mef / MobileElementFinder CLI — follow installed version help
MobileElementFinder -i assembly.fasta -o mef_out
# exact entrypoint may be mefinder / python -m … depending on release

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