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

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dc.contributor.author Prestat, Emmanuel
dc.contributor.author David, Maude M.
dc.contributor.author Hultman, Jenni
dc.contributor.author Taş, Neslihan
dc.contributor.author Lamendella, Regina
dc.contributor.author Dvornik, Jill
dc.contributor.author Mackelprang, Rachel
dc.contributor.author Myrold, David D.
dc.contributor.author Jumpponen, Ari M.
dc.contributor.author Tringe, Susannah G.
dc.contributor.author Holman, Elizabeth
dc.contributor.author Mavromatis, Konstantinos
dc.contributor.author Jansson, Janet K.
dc.date.accessioned 2015-04-21T20:15:42Z
dc.date.available 2015-04-21T20:15:42Z
dc.date.issued 2015-04-21
dc.identifier.uri http://hdl.handle.net/2097/18961
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 http://portal.nersc.gov/project/m1317/FOAM/. en_US
dc.language.iso en_US en_US
dc.relation.uri http://nar.oxfordjournals.org/content/42/19/e145.abstract 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
dc.date.published 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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