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|Alternative name||Functional Ontology Assignments for Metagenomes|
|Restrictions to use||None|
- person_outline Janet K. Jansson
Publication for Functional Ontology Assignments for Metagenomes
Landscape topography structures the soil microbiome in arctic polygonal tundra
[…] ry Table ).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 […]
Databases for Microbiologists
[…] 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 (). […]
Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest
[…] 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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