Introduction

Welcome to the FeGenie wiki!

Nearly all forms of life are dependent on iron for basic cellular maintenance and growth. Microorganisms are often tasked with survival and growth in environments where iron is scantily available. To overcome this challenge, a variety of mechanisms have evolved to allow organisms to compete for whatever small concentration of iron is available. These mechanisms have been widely studied over the past several decades, and while the genetic underpinnings of these mechanisms have been confirmed in many model organisms, the advent of next-generation sequencing and the accumulation of genomic data from novel and uncultivated microorganisms necessitates the development of a systemetized database of genes and gene clusters related to iron utilization. This is the primary focus of this program. We developed a library of profile hidden Markov models (pHMMs) that are representative of all known (as far as we know) iron-related cellular functions, including iron acquisition/transport, iron storage, iron gene regulation, magnetosome formation, and iron reduction/oxidation

FeGenie uses this HMM library to search across provided datasets, and identifies potential homologs and operons that may be linked to the microbial iron cycle Results are summarized in several output files, which include a master summary file, in which users can view the iron genes and iron gene operons that are present in their datasets, and a heatmap-compatible CSV file that summarizes the proportion of each genome that is dedicated to a particular iron-related function.