Helps researchers to explore publicly available sequences harvested from GenBank and assigned to a specific collection of gene families. FGR employs a reference/model-based, comparative analysis strategy to build the reference database and helps to study functional and phylogenetic diversities of specific gene families. This strategy relies on the use of HMMER3 and Hidden Markov Models (HMM). The FGR currently contains 77 gene families organized into seven categories: Antibiotic resistance, Biodegradation, Biogeochemical Cycles, Metal Cycling, Phylogenetic Markers, Plant Pathogenicity, and “Other” for gene families not in the listed categories.
Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA; Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
FGR funding source(s)
This work was supported by grants from the Office of Science (BER), U.S. Department of Energy, Grant DE-FG02-99ER62848 and Bioenergy Center Grant DE-FC02-07ER64494, Superfund Research Program grant P42 ES004911 from the U. S. National Institute of Environmental Health Sciences, National Research Initiative 2008-35107-04542 from the USDA National Institute of Food and Agriculture and NIH Human Microbiome Project Demonstration Project UH3 DK083993.