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

Creator:

Prestat, Emmanuel, David, Maude M., Hultman, Jenni, Taş, Neslihan, Lamendella, Regina, Dvornik, Jill, Mackelprang, Rachel, Myrold, David D., Jumpponen, Ari, Tringe, Susannah G., Holman, Elizabeth, Mavromatis, Konstantinos, and Jansson, Janet K.

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...

Resource Type:

Article
MyroldDavidCropSoilSciFOAMFunctionalOntologyAssignments.pdf

Creator:

Prestat, Emmanuel, David, Maude M., Hultman, Jenni, Myrold, David D., and et al.

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...

Full Text:

., Hultman, J., Taş, N., Lamendella, R., Dvornik, J., ... & Jansson, J. K. (2014). FOAM (Functional Ontology