TitleFOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus.
Publication TypeJournal Article
Year of Publication2014
AuthorsPrestat E, David MM, Hultman J, Taş N, Lamendella R, Dvornik J, Mackelprang R, Myrold DD, Jumpponen A, Tringe SG, Holman E, Mavromatis K, Jansson JK
JournalNucleic Acids Res
Volume42
Issue19
Paginatione145
Date Published2014 Oct 29
ISSN1362-4962
KeywordsBiological Ontologies, Databases, Nucleic Acid, Markov Chains, Metagenome, Metagenomics, Sequence Alignment, Sequence Analysis, Protein, Soil Microbiology
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/.

DOI10.1093/nar/gku702
Alternate JournalNucleic Acids Res.
PubMed ID25260589
PubMed Central IDPMC4231724