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FOAM specifications

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Unique identifier OMICS_05899
Name FOAM
Alternative name Functional Ontology Assignments for Metagenomes
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Janet K. Jansson

Publication for Functional Ontology Assignments for Metagenomes

FOAM citations

 (3)
library_books

Landscape topography structures the soil microbiome in arctic polygonal tundra

2018
Nat Commun
PMCID: 5823929
PMID: 29472560
DOI: 10.1038/s41467-018-03089-z

[…] ry TableĀ ).Prodigal was used to predict coding regions from the single reads. The translated proteins from all detected coding regions of each metagenome were annotated by searching against the FOAM (Functional Ontology Assignments for Metagenomes) database of hidden Markov models generated from Pfam profiles. This screening resulted in the annotation of an average 2.5E+06 to 1.0E+07 genes per sam […]

library_books

Databases for Microbiologists

2015
J Bacteriol
PMCID: 4505447
PMID: 26013493
DOI: 10.1128/JB.00330-15

[…] tabase () positions itself as a comprehensive metagenomic biomining engine by providing the opportunity to find novel homologs of known commercially useful enzymes in metagenomic data sets. The FOAM (Functional Ontology Assignments for Metagenomes) database offers classification of gene functions in environmental metagenomes based on ontology and orthologous relationships (). […]

library_books

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest

2014
PMCID: 4139727
PMID: 24722629
DOI: 10.1038/ismej.2014.36

[…] regions of each metagenome were annotated by searching against a custom in-house database (Prestat et al., in review) of hidden Markov models generated from Pfam profiles (Release 26.0; ). The FOAM (Functional Ontology Assignments for Metagenomes) database is publically available at (http://portal.nersc.gov/project/m1317/FOAM/). Microbial functions that contribute to soil biogeochemical cycles we […]


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FOAM institution(s)
Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Division of Biology, Kansas State University, Manhattan, Kansas, USA; DOE Joint Genome Institute, Walnut Creek, CA, USA; Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA; DOE Joint Bioenergy Institute, Emeryville, CA, USA; Department of Plant and Microbial Biology, University of California, Berkeley, USA; Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, Denmark

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