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 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...
Social media platforms use many techniques to engage users' attention with their platforms, including notifications, popups, and gamification elements. The impact of social media on physical and mental health has been studied, but limited publicly available research exists on how social media users can be helped to disengage from these...
This paper reports the findings of two studies conducted at Oregon State University. The first set of studies compares use of header comments versus mnemonic procedure and function names by programmers performing tasks relating to modification tasks. The second study compares the use of header comments versus in-line comments when...
Creating effective packaging is about finding a balance between product protection during shipping and time consumption in the design process. Given time and cost constraints, it is hard to produce sufficiently protective padding while having it not be thicker than it needs to be. This thesis describes a method to...
Steel moment-resisting frames (MRFs) are widely used in the United States to resist seismic forces. MRFs have many advantages, including architectural versatility, vetted member and connection detailing requirements, and high ductility for special MRFs (SMRF). However, MRFs require large members to meet story drift criteria. Moreover, strong-column-weak-beam requirements can result...
In order to generate practical ways to easily design functional flexible lattice structures, this research seeks to find a way to predict reactive forces of compressed hyperelastic cubic lattice structures. Using 3D printed test coupons, material data was collected for use in finite element analysis. Cubic lattice structures with varying...
Magnetic susceptibility (MS) is a measure of a sample material's ability to be magnetized by an applied magnetic field. Applied to sedimentology, it provides us with a proxy indicator for the concentration of magnetizable minerals present at each depth. This knowledge, in conjunction with directional magnetic alignment data, climatic histories,...
The scattering of optical rays by small spherical particles bears a strong resemblance to the
diffusion of fission neutrons in solid materials. This work explores the feasibility of
exploiting similarities between these two systems for the purposes of reactor component analysis, education, and outreach. After a brief overview of reactor-environment...