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...
Full Text:
Metagenomes): a Hidden
Markov Model (HMM) database with environmental focus
Prestat, E., David, M. M
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...
Classical radiative transfer programs are based on the plane-parallel assumption. We show that the Gershun equation is valid if the irradiance is averaged over a sufficiently large area. We show that the equation is invalid for horizontal areas of the order of tens of meters in which horizontal gradients of...
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...
Satellite measurements allow global assessments of phytoplankton concentrations and, from observed temporal changes in biomass, direct access to net biomass accumulation rates (r). For the subarctic Atlantic basin, analysis of annual cycles in r reveals that initiation of the annual blooming phase does not occur in spring after stratification surpasses...
The three-dimensional structure and the origin of mesoscale anticyclonic
intrathermocline eddies (ITEs) in the coastal transition zone (CTZ) off central Chile (31–41°S) were analyzed through the combination of data from oceanographic cruises and
satellite altimetry, and the application of an eddy-resolving primitive equation ocean model
coupled with a numerical experiment...
We investigated 32 net primary productivity (NPP) models by assessing skills to reproduce integrated NPP in the Arctic Ocean. The models were provided with two sources each of surface chlorophyll-a concentration (chlorophyll), photosynthetically available radiation (PAR), sea surface temperature (SST), and mixed-layer depth (MLD). The models were most sensitive to...
Acidified waters are impacting commercial oyster
production in the U.S. Pacific Northwest, and favorable
carbonate chemistry conditions are predicted to become
less frequent. Within 48 h of fertilization, unshelled Pacific
oyster (Crassostrea gigas) larvae precipitate roughly 90% of
their body weight as calcium carbonate. We measured stable
carbon isotopes in...
Curbing overall disease burden with faster intervention requires early stage and accurate diagnostics. Ultrasound (US) provides a safe, nonionizing, inexpensive, and noninvasive imaging modality that has become commonplace in diagnostics. Paired with the relatively new technology of photoacoustic imaging (PAI), optical level resolution becomes feasible with the deeper signal penetration...