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Netprimer
NetPrimer is a gratis web-based tool used for analysing Primer (molecular biology), primers used in Polymerase chain reaction, PCR to amplify a DNA sequence. The software predicts the melting temperature of the primers using the nearest neighbor thermodynamic algorithm. The accurate prediction of the melting temperature (Tm) is one of the most important factors that governs the success of a PCR reaction. NetPrimer also analyzes the thermodynamically important secondary structures such as stem loop, hairpins, self and cross primer dimer, dimers, runs and repeats. These structures significantly affect the primer efficiency and therefore the success of a PCR reaction. NetPrimer can be used to determine the best primer pairs for a given set of experimental conditions. The program assigns a rating to each primer analyzed. The rating is based on the proximity of the thermodynamic parameters to their ideal scores. In addition to the primer quality, its molecular weight and Nucleic acid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
6 May 2002
6 (six) is the natural number following 5 and preceding 7. It is a composite number and the smallest perfect number. In mathematics Six is the smallest positive integer which is neither a square number nor a prime number; it is the second smallest composite number, behind 4; its proper divisors are , and . Since 6 equals the sum of its proper divisors, it is a perfect number; 6 is the smallest of the perfect numbers. It is also the smallest Granville number, or \mathcal-perfect number. As a perfect number: *6 is related to the Mersenne prime 3, since . (The next perfect number is 28 (number), 28.) *6 is the only even perfect number that is not the sum of successive odd cubes. *6 is the root of the 6-aliquot tree, and is itself the aliquot sum of only one other number; the square number, . Six is the only number that is both the sum and the product of three consecutive positive numbers. Unrelated to 6's being a perfect number, a Golomb ruler of length 6 is a "perfect ruler". Si ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java Applet
Java applets were small applications written in the Java programming language, or another programming language that compiles to Java bytecode, and delivered to users in the form of Java bytecode. The user launched the Java applet from a web page, and the applet was then executed within a Java virtual machine (JVM) in a process separate from the web browser itself. A Java applet could appear in a frame of the web page, a new application window, Sun's AppletViewer, or a stand-alone tool for testing applets. Java applets were introduced in the first version of the Java language, which was released in 1995. Beginning in 2013, major web browsers began to phase out support for the underlying technology applets used to run, with applets becoming completely unable to be run by 2015–2017. Java applets were deprecated by Java 9 in 2017. Java applets were usually written in Java, but other languages such as Jython, JRuby, Pascal, Scala, NetRexx, or Eiffel (via ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms ( SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable propertie ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Primer (molecular Biology)
Primer may refer to: Arts, entertainment, and media Films * ''Primer'' (film), a 2004 feature film written and directed by Shane Carruth * ''Primer'' (video), a documentary about the funk band Living Colour Literature * Primer (textbook), a textbook used in primary education to teach the alphabet and other basic subjects * Primer (prayer book), a common name for English prayer books used from the 13th to 16th centuries * '' The New England Primer'' (1688), a Puritan book from Colonial America with morality-themed rhymes Music * ''Primer'' (album), a 1995 music album by the musical group Rockapella * Primer 55, an American alternative metal band * "The Primer", a song from the 2005 album ''Alaska'' by Between the Buried and Me Firearms * Primer (firearms), a firearm powder charge-ignition mechanism ** Centerfire ammunition, Boxer or Berdan primers used in modern centerfire cartridges ** Detonator, a small explosive device also known as an explosive primer or blasting cap ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polymerase Chain Reaction
The polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) to a large enough amount to study in detail. PCR was invented in 1983 by the American biochemist Kary Mullis at Cetus Corporation; Mullis and biochemist Michael Smith, who had developed other essential ways of manipulating DNA, were jointly awarded the Nobel Prize in Chemistry in 1993. PCR is fundamental to many of the procedures used in genetic testing and research, including analysis of ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory research for a broad variety of applications including biomedical research ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nearest Neighbor Thermodynamic Algorithm
Nucleic acid thermodynamics is the study of how temperature affects the nucleic acid structure of double-stranded DNA (dsDNA). The melting temperature (''Tm'') is defined as the temperature at which half of the DNA strands are in the random coil or single-stranded (ssDNA) state. ''Tm'' depends on the length of the DNA molecule and its specific nucleotide sequence. DNA, when in a state where its two strands are dissociated (i.e., the dsDNA molecule exists as two independent strands), is referred to as having been denatured by the high temperature. Concepts Hybridization Hybridization is the process of establishing a non-covalent, sequence-specific interaction between two or more complementary strands of nucleic acids into a single complex, which in the case of two strands is referred to as a duplex. Oligonucleotides, DNA, or RNA will bind to their complement under normal conditions, so two perfectly complementary strands will bind to each other readily. In order to reduce the div ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Secondary Structure
Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was first introduced by Kaj Ulrik Linderstrøm-Lang at Stanford in 1952. Other types of biopolymers such as nucleic acids also possess characteristic secondary structures. Types The most common secondary st ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stem Loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. As an important secondary structure of RNA, it can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA binding proteins, and serve as a substrate for enzymatic reactions. Formation and stability The formation of a stem-loop structure is dependent on the stability of the resulting helix and loop regions. The first prerequisite is the presence of a sequence that can fold back on itself to form a paired double helix. The stability of this helix is determined by its length, the number of mismatches or bulges it ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Primer Dimer
A primer dimer (PD) is a potential by-product in the polymerase chain reaction (PCR), a common biotechnological method. As its name implies, a PD consists of two primer molecules that have attached ( hybridized) to each other because of strings of complementary bases in the primers. As a result, the DNA polymerase amplifies the PD, leading to competition for PCR reagents, thus potentially inhibiting amplification of the DNA sequence targeted for PCR amplification. In quantitative PCR, PDs may interfere with accurate quantification. Mechanism of formation A primer dimer is formed and amplified in three steps. In the first step, two primers anneal at their respective 3' ends (step I in the figure). If this construct is stable enough, the DNA polymerase will bind and extend the primers according to the complementary sequence (step II in the figure). An important factor contributing to the stability of the construct in step I is a high GC-content at the 3' ends and length of the ove ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Weight
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and ''molecule'' is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term ''molecule'' is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid Quantitation
In molecular biology, quantitation of nucleic acids is commonly performed to determine the average concentrations of DNA or RNA present in a mixture, as well as their purity. Reactions that use nucleic acids often require particular amounts and purity for optimum performance. To date, there are two main approaches used by scientists to quantitate, or establish the concentration, of nucleic acids (such as DNA or RNA) in a solution. These are spectrophotometric quantification and UV fluorescence tagging in presence of a DNA dye. Spectrophotometric analysis One of the most commonly used practices to quantitate DNA or RNA is the use of spectrophotometric analysis using a spectrophotometer. A spectrophotometer is able to determine the average concentrations of the nucleic acids DNA or RNA present in a mixture, as well as their purity. Spectrophotometric analysis is based on the principles that nucleic acids absorb ultraviolet light in a specific pattern. In the case of DNA a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nmol
The mole, symbol mol, is the unit of amount of substance in the International System of Units (SI). The quantity amount of substance is a measure of how many elementary entities of a given substance are in an object or sample. The mole is defined as containing exactly elementary entities. Depending on what the substance is, an elementary entity may be an atom, a molecule, an ion, an ion pair, or a subatomic particle such as an electron. For example, 10 moles of water (a chemical compound) and 10 moles of mercury (a chemical element), contain equal amounts of substance and the mercury contains exactly one atom for each molecule of the water, despite the two having different volumes and different masses. The number of elementary entities in one mole is known as the Avogadro number, which is the approximate number of nucleons ( protons or neutrons) in one gram of ordinary matter. The previous definition of a mole was simply the number of elementary entities equal to that of 12 gr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
