FOAM

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden
Markov Model (HMM) database with environmental focus
(http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku702.full)
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.
Availability
HMMs | |
Ontology | |
Alignments | |
README |