title: FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus.
abstract: A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. 'profiles') were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/.
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Prestat
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Maude M
authors.initials: MM
authors.lastname: David
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Jenni
authors.initials: J
authors.lastname: Hultman
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Neslihan
authors.initials: N
authors.lastname: Taş
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Regina
authors.initials: R
authors.lastname: Lamendella
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Jill
authors.initials: J
authors.lastname: Dvornik
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Mackelprang
authors.affiliation: Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA.
authors.forename: David D
authors.initials: DD
authors.lastname: Myrold
authors.affiliation: Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA.
authors.forename: Ari
authors.initials: A
authors.lastname: Jumpponen
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Susannah G
authors.initials: SG
authors.lastname: Tringe
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Holman
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA DOE Joint Genome Institute, Walnut Creek, CA 94598, USA DOE Joint Bioenergy Institute, Emeryville, CA 94608, USA Department of Plant and Microbial Biology, University of California, Berkeley 94720, USA Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen 1017, Denmark janet.jansson@pnnl.gov.
authors.forename: Janet K
authors.initials: JK
authors.lastname: Jansson
mesh_terms: D064229:Biological Ontologies; D030561:Databases, Nucleic Acid; D008390:Markov Chains; D054892:Metagenome; D056186:Metagenomics; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012988:Soil Microbiology