FeGenie

FeGenie identifies and annotates genes involved in microbial iron metabolism in genome and metagenome assemblies using a curated hidden Markov model (HMM) database.

Key Features:

• Curated Iron-Related HMM Database: Uses a curated and regularly updated set of HMMs targeting genes associated with iron oxidation, dissimilatory iron reduction, and other iron-related biological processes.
• HMMER and BLAST-Based Gene Detection: Detects iron metabolism genes and analyzes gene neighborhoods using HMMER and BLAST with multi-threading support.
• Genome and Metagenome Compatibility: Processes isolate genomes and environmental metagenome assemblies to profile iron gene repertoires.

Scientific Applications:

• Microbial Iron Cycling Analysis: Characterizes iron oxidation and reduction potential in environmental and host-associated microbial communities to investigate ecological roles and iron availability correlations.

Methodology:

FeGenie applies HMM-based searches with HMMER and complementary BLAST analyses to genome and metagenome assemblies, annotating iron-related genes and genomic contexts to infer microbial iron metabolic potential.