An Operational Taxonomic Unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by and Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "Operational Taxonomic Unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern evolutionary taxonomy. Nowadays, however, the term "OTU" is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "species" (microbial or metazoan) at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) marker gene sequence datasets. Sequences can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold (usually 97% similarity; however also 100% similarity is common, also known as single variants) set by the researcher. It remains debatable how well this commonly-used method recapitulates true microbial species phylogeny or ecology. Although OTUs can be calculated differently when using different algorithms or thresholds, recent research by Schmidt et al. (2014) demonstrated that microbial OTUs were generally ecologically consistent across habitats and several OTU clustering approaches. The number of OTUs defined may be inflated due to errors in DNA sequencing. (Wikipedia).
Overview of Experimental Design
From playlist Unit 4: Sampling and Experimental Design
Percentiles, Deciles, Quartiles
Understanding percentiles, quartiles, and deciles through definitions and examples
From playlist Unit 1: Descriptive Statistics
Determining values of a variable at a particular percentile in a normal distribution
From playlist Unit 2: Normal Distributions
More Standard Deviation and Variance
Further explanations and examples of standard deviation and variance
From playlist Unit 1: Descriptive Statistics
Mean v Median and the implications
Differences between the mean and median suggest the presence of outliers and/or the possible shape of a distribution
From playlist Unit 1: Descriptive Statistics
Operating system for beginners || Operating system basics
An operating system (OS) is system software that manages computer hardware, software resources, and provides common services for computer programs. Time-sharing #operating_systems schedule tasks for efficient use of the system and may also include accounting software for cost allocation o
From playlist Operating System
FROGS Find Rapidly OTU with Galaxy Solution, 20160628
Galaxy Community Conference 2016, Indiana University - Bloomington | https://gcc2016.iu.edu/ https://gcc16.sched.com/event/3708f8eb14531cffedf3c29aed075a43# Authors: Frederic ESCUDIE, INRA Toulouse Lucas AUER, INRA Toulouse Maria BERNARD, INRA Jouy-en-Josas Laurent CAUQUIL, INRA Toulouse
From playlist 2016 Galaxy User Community Conference (GCC16)
David Koslicki: "The CAMI Project: Assessment of computational techniques in metagenomics"
Computational Genomics Summer Institute 2017 Tutorial: "The CAMI Project: Assessment of computational techniques in metagenomics" David Koslicki, Oregon State University Institute for Pure and Applied Mathematics, UCLA July 12, 2017 For more information: http://computationalgenomics.bio
From playlist Computational Genomics Summer Institute 2017
Moodle - Add an Assignment activity
From playlist Training - Moodle
An overview and introduction to understanding sampling distributions of proportions [sample proportions] and how to calculate them
From playlist Unit 7 Probability C: Sampling Distributions & Simulation
Evolution, Biogeography and "Systems Ecology" in Microbial Eukaryote Taxa - H. Bik - 1/14/16
Bioinformatics Research Symposium Beckman Institute Auditorium Thursday, January 14, 2016
From playlist Bioinformatics Research Symposium
Elizabeth Ramirez - Graph Database Patterns in Python - PyCon 2015
"Speaker: Elizabeth Ramirez Creating and using models from a graph database can be quite different to the ones used for row/column/document-oriented databases, in the sense that the same query patterns could differ significantly in structure and performance. This session will present how
From playlist Software Development Lectures
Live CEOing Ep 681: Language Design in Wolfram Language [Ontologies]
In this episode of Live CEOing, Stephen Wolfram discusses upcoming improvements and features to the Wolfram Language. If you'd like to contribute to the discussion in future episodes, you can participate through this YouTube channel or through the official Twitch channel of Stephen Wolfram
From playlist Behind the Scenes in Real-Life Software Design
Why Hardwoods Are The Softest Woods
Use the promo code "minuteearth" at https://curiositystream.com/minuteearth for 26% off an annual subscription to CuriosityStream, plus access to Nebula! Not all hardwood trees have hard wood and softwoods soft wood, because these terms denote their taxonomic ancestry, not the wood's actu
From playlist Evolution
Knowledgebase Query Language and Entities
This webinar features talks that demonstrate how Version 12 of the Wolfram Language extends the capabilities of the entity framework, with a deeper look at food and nutrition data, cultural and historical entities and computable knowledge in biology and medicine. This is the second webinar
From playlist New in Wolfram Language 12 Webinar Series
Laplace transform of f(t-a)u(t-a), the shifted unit step function
laplace transform of unit step function, Laplace transform of f(t-a)u(t-a), Laplace transform of the shifted unit step function, Laplace transform of f(t)u(t-a), Translation in t theorem, differential equation and laplace transform, www.blackpenredpen.com
From playlist Unit Step Functions & Translation in t (Nagle Sect7.6)
Introduction to standard deviation, IQR [Inter-Quartile Range], and range
From playlist Unit 1: Descriptive Statistics
New Biology Content in the Wolfram Language
Wolfram technology provides access to a diverse range of computable knowledge about biology. In this talk, topics such as taxonomic classifications, dinosaurs and genomics are explored as examples of the breadth of information available in the Wolfram Language. The latest taxonomic data co
From playlist Wolfram Technology Conference 2022