| name | fegenie |
| description | FeGenie — HMM-based identification of iron-related genes and neighborhoods in genomes/metagenome assemblies (acquisition, siderophores, Fe redox, storage, magnetosome). Use for Fe cycling potential on contigs or MAGs. Upstream: https://github.com/Arkadiy-Garber/FeGenie. Route via element-cycling / microbial-mining. Broader C/N/S → metabolic; S scores → mebs.
|
| license | MIT |
| category | analysis-tools |
| tags | ["FeGenie","iron","Fe","siderophore","biogeochemistry","element-cycling"] |
| upstream | https://github.com/Arkadiy-Garber/FeGenie |
| stage | mining |
FeGenie
Upstream: Arkadiy-Garber/FeGenie
Citation
Garber, A. I. et al. FeGenie: A Comprehensive Tool for the Identification of
Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies.
Front. Microbiol. 11, 37 (2020).
https://doi.org/10.3389/fmicb.2020.00037
See also docs/references.md.
Analytical thinking
FeGenie targets iron: transport/acquisition, siderophores, oxidation /
dissimilatory reduction, storage, magnetosome-related genes, and neighborhoods.
Complements generic KO annotation that often misses Fe redox markers.
| vs | Prefer FeGenie when |
|---|
metabolic / dram | Fe-specific gene families and operon context |
mebs | Explicit Fe gene calls vs cycle entropy scores |
antismash | Siderophore BGC context vs FeGenie HMM categories |
Hits ≠ demonstrated Fe flux or siderophore production.
How to run
Decision tree
Iron / siderophore genetic potential?
├─ Yes → fegenie
├─ Multi-element C/N/S diagrams → metabolic
├─ S/N/CH₄/Fe scores → mebs
└─ Broad distillate → dram
Related skills
element-cycling · metabolic · mebs · dram · antismash ·
microbial-mining · tool-selection
