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

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/.
Authors:
 [1] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [2] ;  [6] ;  [7]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kansas State Univ., Manhattan, KS (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); DOE Joint Genome Institute, Walnut Creek, CA (United States)
  4. Oregon State Univ., Corvallis, OR (United States)
  5. Kansas State Univ., Manhattan, KS (United States)
  6. DOE Joint Genome Institute, Walnut Creek, CA (United States)
  7. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); DOE Joint Genome Institute, Walnut Creek, CA (United States); DOE Joint Bioenergy Institute, Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States); Univ. of Copenhagen, Copenhagen (Denmark)
Publication Date:
OSTI Identifier:
1213416
Grant/Contract Number:
SC0004953; AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 42; Journal Issue: 19; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Research Org:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES