ArticleNucleic acids research2014
FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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60 citing papers in PubMed.
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- Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila.Frontiers in microbiology · 2024Article
- Tracing active members in microbial communities by BONCAT and click chemistry-based enrichment of newly synthesized proteins.ISME communications · 2024Article
- Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects.Environmental microbiology reports · 2023Article
- Distribution and Activity of Sulfur-Metabolizing Bacteria along the Temperature Gradient in Phototrophic Mats of the Chilean Hot Spring Porcelana.Microorganisms · 2023Article
- RNA Viruses Linked to Eukaryotic Hosts in Thawed Permafrost.mSystems · 2022Article
- Structural characterization of a soil viral auxiliary metabolic gene product - a functional chitosanase.Nature communications · 2022Article
- Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes.Scientific reports · 2022Article
- How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research.Microorganisms · 2022Review
- Ecosystem-specific microbiota and microbiome databases in the era of big data.Environmental microbiome · 2022Review
- ROCker Models for Reliable Detection and Typing of Short-Read Sequences Carrying β-Lactamase Genes.mSystems · 2022Article
- Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples.Microbiology spectrum · 2022Article
- Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides.Nature communications · 2022Article
- Microbial drivers of methane emissions from unrestored industrial salt ponds.The ISME journal · 2022Article
- Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing.Journal of animal science · 2022Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
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/.
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