fegenie

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

# follow upstream README / wiki Tutorial — folder of genome or assembly FASTA
# provide bundled HMM library + bitscore cutoffs; pin FeGenie commit + HMM set

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