FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus

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Show simple item record Prestat, Emmanuel David, Maude M. Hultman, Jenni Taş, Neslihan Lamendella, Regina Dvornik, Jill Mackelprang, Rachel Myrold, David D. Jumpponen, Ari M. Tringe, Susannah G. Holman, Elizabeth Mavromatis, Konstantinos Jansson, Janet K. 2015-04-21T20:15:42Z 2015-04-21T20:15:42Z 2015-04-21
dc.description.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 en_US
dc.language.iso en_US en_US
dc.relation.uri en_US
dc.rights This article was originally published in Nucleic Acids Research, Oxford University Press. en_US
dc.subject Gene database en_US
dc.subject Metagenomes en_US
dc.subject Functional ontology en_US
dc.subject Hidden Markov Models en_US
dc.title FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus en_US
dc.type Article (publisher version) en_US 2014 en_US
dc.citation.doi doi:10.1093/nar/gku702 en_US
dc.citation.issue 19 en_US
dc.citation.jtitle Nucleic Acids Research en_US
dc.citation.spage e145 en_US
dc.citation.volume 42 en_US
dc.contributor.authoreid ari en_US

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