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QIIME
QIIME (an abbreviation for ''Quantitative Insights Into Microbial Ecology'') is a bioinformatic pipeline designated for the task of analysing microbial communities that were sampled through marker gene (e.g. 16S or 18S rRNA genes) amplicon sequencing. In its heart the pipeline performs quality control over the input sequencing reads, clusters the marker gene nucleotide sequences at a requested phylogenetic level (e.g. 97% for species level) into OTUs (operational taxonomic units) or sequence variants and taxonomically annotates them by looking for similar sequences in a reference taxonomic database. The main output from the QIIME pipeline is a feature table, which describes the abundances of each OTU or sequence variant in each sample. Additional tools that are relevant to ecological aspects of the samples being investigated are also provided within the pipeline, including rarefaction, alpha diversity and beta diversity calculations, visualizations such as principle coordinates ana ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
16S Ribosomal RNA
16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S rRNA gene and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene. Carl Woese and George E. Fox were two of the people who pioneered the use of 16S rRNA in phylogenetics in 1977. Multiple sequences of the 16S rRNA gene can exist within a single bacterium. Functions * Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal proteins. * The 3-end contains the anti- Shine-Dalgarno sequence, which binds upstream to the AUG start codon on the mRNA. The 3-end of 16S RNA binds to the proteins S1 and S21 which are known to be involved in initiation of protein synthesis * Interacts with 23S, aiding in the binding of the two ribosomal s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microbial
A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in older texts. The informal synonym ''microbe'' () comes from μικρός, mikrós, "small" and βίος, bíos, "life". is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells. The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from sixth century BC India. The scientific study of microorganisms began with their observation under the microscope in the 1670s by Anton van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera, diphtheria, and anthrax. Because mi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alpha Diversity
In ecology, alpha diversity (α-diversity) is the mean species diversity in a site at a local scale. The term was introduced by R. H. WhittakerWhittaker, R. H. (1960) Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monographs, 30, 279–338. Whittaker, R. H. (1972). Evolution and Measurement of Species Diversity. Taxon, 21, 213-251. together with the terms beta diversity (β-diversity) and gamma diversity (γ-diversity). Whittaker's idea was that the total species diversity in a landscape (gamma diversity) is determined by two different things, the mean species diversity in sites at a more local scale (alpha diversity) and the differentiation among those sites (beta diversity). Scale considerations Both the area or landscape of interest and the sites within it may be of very different sizes in different situations, and no consensus has been reached on what spatial scales are appropriate to quantify alpha diversity. It has therefore been proposed that the de ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microbial Ecology
Microbial ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (calculated as cells; eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Marker Gene
In biology, a marker gene may have several meanings. In nuclear biology and molecular biology, a marker gene is a gene used to determine if a nucleic acid sequence has been successfully inserted into an organism's DNA. In particular, there are two sub-types of these marker genes: a selectable marker and a marker for screening. In metagenomics and phylogenetics, a marker gene is an Sequence_homology#Orthology, orthologous gene group which can be used to delineate between taxonomic lineages. Selectable marker A selectable marker protects the organism from a ''selective agent'' that would normally kill it or prevent its growth. In a transformation reaction, depending on the transformation efficiency, only one in several million to billion cells may take up DNA. Rather than checking every single cell, scientists use a selective agent to kill all cells that do not contain the foreign DNA, leaving only the desired ones. Antibiotics are the most common selective agents. In bacteria, a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BLAST
Blast or The Blast may refer to: * Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film), starring Andrew Divoff * ''Blast'' (2000 film), starring Liesel Matthews * ''Blast'' (2004 film), an action comedy film * ''Blast!'' (1972 film) or ''The Final Comedown'', an American drama * ''BLAST!'' (2008 film), a documentary about the BLAST telescope * '' A Blast'', a 2014 film directed by Syllas Tzoumerkas Magazines * ''Blast'' (magazine), a 1914–15 literary magazine of the Vorticist movement * ''Blast'' (U.S. magazine), a 1933–34 American short-story magazine * ''The Blast'' (magazine), a 1916–17 American anarchist periodical Music * Blast (American band), a hardcore punk band * Blast (Russian band), an indie band * ''Blast'' (album), by Holly Johnson, 1989 * ''The Blast'' (album), by Yuvan Shankar Raja, 1999 * " ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UCLUST
UCLUST is an algorithm designed to cluster nucleotide or amino-acid sequences into clusters based on sequence similarity. The algorithm was published in 2010 and implemented in a program also named UCLUST. The algorithm is described by the author as following two simple clustering criteria, in regard to the requested similarity threshold T. The first criterion states that any given cluster's centroid sequence will have a similarity smaller than T to any other clusters' centroid sequence. The second criterion states that each member sequence in a given cluster will have similarity to the cluster's centroid sequence that is equal or greater than T. UCLUST algorithm is a greedy one. As a result, the order of the sequences in the input file will affect the resulting clusters and their quality. For this reason, it is advised that the sequences will be sorted before entering clustering stage. The program UCLUST is equipped with some options to sort the input sequences prior to clustering ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multidimensional Scaling
Multidimensional scaling (MDS) is a means of visualizing the level of similarity of individual cases of a dataset. MDS is used to translate "information about the pairwise 'distances' among a set of n objects or individuals" into a configuration of n points mapped into an abstract Cartesian space. More technically, MDS refers to a set of related ordination techniques used in information visualization, in particular to display the information contained in a distance matrix. It is a form of non-linear dimensionality reduction. Given a distance matrix with the distances between each pair of objects in a set, and a chosen number of dimensions, ''N'', an MDS algorithm places each object into ''N''-dimensional space (a lower-dimensional representation) such that the between-object distances are preserved as well as possible. For ''N'' = 1, 2, and 3, the resulting points can be visualized on a scatter plot. Core theoretical contributions to MDS were made by James O. Ramsay of M ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Diversity
Beta (, ; uppercase , lowercase , or cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents the voiced labiodental fricative while in borrowed words is instead commonly transcribed as μπ. Letters that arose from beta include the Roman letter and the Cyrillic letters and . Name Like the names of most other Greek letters, the name of beta was adopted from the acrophonic name of the corresponding letter in Phoenician, which was the common Semitic word ''*bait'' ('house'). In Greek, the name was ''bêta'', pronounced in Ancient Greek. It is spelled βήτα in modern monotonic orthography and pronounced . History The letter beta was derived from the Phoenician letter beth . Uses Algebraic numerals In the system of Greek numerals, beta has a value of 2. Such use is denoted by a number mark: Β′. Computing Finance Beta is used i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Taxonomically
In biology, taxonomy () is the scientific study of naming, defining ( circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (''division'' is sometimes used in botany in place of ''phylum''), class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms. With advances in the theory, data and analytical technology of biological systematics, the Linnaean system has transformed into a system of modern biological classification intended to reflect the evo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rarefaction
Rarefaction is the reduction of an item's density, the opposite of compression. Like compression, which can travel in waves (sound waves, for instance), rarefaction waves also exist in nature. A common rarefaction wave is the area of low relative pressure following a shock wave (see picture). Rarefaction waves expand with time (much like sea waves spread out as they reach a beach); in most cases rarefaction waves keep the same overall profile ('shape') at all times throughout the wave's movement: it is a ''self-similar expansion''. Each part of the wave travels at the local speed of sound, in the local medium. This expansion behaviour contrasts with that of pressure increases, which gets narrower with time until they steepen into shock waves. When angle of incidence is greater than angle of refraction, then light travels from denser to rarer medium. When angle of incidence is smaller than angle of refraction then light travels from rarer to denser medium Physical examples A nat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Communities
A community is a Level of analysis, social unit (a group of living things) with commonality such as place (geography), place, Norm (social), norms, religion, values, Convention (norm), customs, or Identity (social science), identity. Communities may share a sense of place (geography), place situated in a given geographical area (e.g. a country, village, town, or neighbourhood) or in virtual space through communication platforms. Durable good relations that extend beyond immediate genealogical ties also define a sense of community, important to their identity, practice, and roles in social institutions such as family, home, work, government, society, or humanity at large. Although communities are usually small relative to personal social ties, "community" may also refer to large group affiliations such as nation, national communities, international community, international communities, and virtual community, virtual communities. The English-language word "community" derives from ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
