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Phred (software)
Phred is a computer program for base calling, that is to say, identifying a nucleobase sequence from fluorescence "trace" data generated by an automated DNA sequencer that uses electrophoresis and 4-fluorescent dye method. When originally developed, Phred produced significantly fewer errors in the data sets examined than other methods, averaging 40–50% fewer errors. Phred quality scores have become widely accepted to characterize the quality of DNA sequences, and can be used to compare the efficacy of different sequencing methods. Background The fluorescent-dye DNA sequencing is a molecular biology technique that involves labeling single-strand DNA sequences of varied length with 4 fluorescent dyes (corresponding to 4 different Nucleobase, bases used in DNA) and subsequently separating the DNA sequences by "slab gel"- or capillary-electrophoresis method (see DNA Sequencing). The electrophoresis run is monitored by a Charge-coupled device, CCD on the DNA sequencer and this produc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Base Calling
Base calling is the process of assigning nucleobases to chromatogram peaks, light intensity signals, or electrical current changes resulting from nucleotides passing through a nanopore. One computer program for accomplishing this job is Phred (software), Phred, which is a widely used base calling software program by both academic and commercial DNA sequencing laboratories because of its high base calling accuracy. Base callers for Nanopore sequencing use neural networks trained on current signals obtained from accurate sequencing data. Base calling accuracy Base calling can be assessed by two metrics, read accuracy and consensus accuracy. Read accuracy refers to the called base's accuracy to a known reference. Consensus accuracy refers to how accurate a consensus sequence is compared to overlapping reads from the same genetic locus. References {{reflist Molecular biology Bioinformatics ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chromatogram
In chemical analysis, chromatography is a laboratory technique for the separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it through a system (a column, a capillary tube, a plate, or a sheet) on which a material called the ''stationary phase'' is fixed. Because the different constituents of the mixture tend to have different affinities for the stationary phase and are retained for different lengths of time depending on their interactions with its surface sites, the constituents travel at different apparent velocities in the mobile fluid, causing them to separate. The separation is based on the differential partitioning between the mobile and the stationary phases. Subtle differences in a compound's partition coefficient result in differential retention on the stationary phase and thus affect the separation. Chromatography may be preparative or analytical. The purpose of preparativ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phrap
Phrap is a widely used program for DNA sequence assembly. It is part of the Phred-Phrap-Consed package. History Phrap was originally developed by Prof. Phil Green for the assembly of cosmids in large-scale cosmid shotgun sequencing within the Human Genome Project. Phrap has been widely used for many different sequence assembly projects, including bacterial genome assemblies and EST assemblies. Phrap was written as a command line program for easy integration into automated data workflows in genome sequencing centers. For users who want to use Phrap from a graphical interface, the commercial programs MacVector (for Mac OS X only) and CodonCode Aligner (for Mac OS X and Microsoft Windows) are available. Methods A detailed (albeit partially outdated) description of the Phrap algorithms can be found in thPhrap documentation A recurring thread within the Phrap algorithms is the use of Phred quality scores. Phrap used quality scores to mitigate a problem that other assembly progra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MacVector
MacVector is a commercial sequence analysis application for Apple Macintosh computers running Mac OS X. It is intended to be used by Molecular biology, molecular biologists to help analyze, design, research and document their experiments in the laboratory. MacVector 18.1 is a Universal binary, Universal Binary capable of running on Intel and Apple Silicon Macs. Features MacVector is a collection of sequence analysis algorithms linked to various sequence editors, including a single sequence editor, a multiple sequence alignment editor and a contig editor. MacVector tries to use a minimum of windows and steps to access all the functionality. Functions include: * Sequence alignment (ClustalW, MUSCLE (alignment software), Muscle and T-COFFEE, T-Coffee) and editing. * Subsequence search and open reading frames (ORFs) analysis. * Phylogenetic tree construction UPGMA, Neighbour joining with bootstrapping and consensus trees * Online Database searching - Search public databases at the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CodonCode Aligner
CodonCode Aligner is a commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows. Features Features include chromatogram editing, end clipping, and vector trimming, sequence assembly and contig editing, aligning cDNA against genomic templates, sequence alignment and editing, alignment of contigs to each other with ClustalW, MUSCLE, or built-in algorithms, mutation detection, including detection of heterozygous single-nucleotide polymorphism, analysis of heterozygous insertions and deletions, start online BLAST searches, restriction analysis (find and view restriction cut sites), trace sharpening, and support for Phred, Phrap, ClustalW, and MUSCLE. History The first beta version of CodonCode Aligner was released in April 2003, followed by the first full version in June 2003. Major upgrades were released in 2003, 2004, 2005, 2006, 2007, and 2008. In April 2009, CodonCode Aligner had been cited in more than 400 scientific publi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Human Genome Project
The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a physical and a functional standpoint. It started in 1990 and was completed in 2003. It remains the world's largest collaborative biological project. Planning started after the idea was picked up in 1984 by the US government, the project formally launched in 1990, and was declared essentially complete on April 14, 2003, but included only about 85% of the genome. Level "complete genome" was achieved in May 2021, with a remaining only 0.3% bases covered by potential issues. The final gapless assembly was finished in January 2022. Funding came from the United States government through the National Institutes of Health (NIH) as well as numerous other groups from around the world. A parallel project was conducted outside the government by the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of Washington
The University of Washington (UW, simply Washington, or informally U-Dub) is a public research university in Seattle, Washington. Founded in 1861, Washington is one of the oldest universities on the West Coast; it was established in Seattle approximately a decade after the city's founding. The university has a 703 acre main campus located in the city's University District, as well as campuses in Tacoma and Bothell. Overall, UW encompasses over 500 buildings and over 20 million gross square footage of space, including one of the largest library systems in the world with more than 26 university libraries, art centers, museums, laboratories, lecture halls, and stadiums. The university offers degrees through 140 departments, and functions on a quarter system. Washington is the flagship institution of the six public universities in Washington state. It is known for its medical, engineering, and scientific research. Washington is a member of the Association of American Universiti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Richard Mott (statistician)
Richard Mott is Weldon Professor of Computational and Statistical Genetics in the research department of Genetics, Evolution and Environment at University College London. He was previously at the Wellcome Centre for Human Genetics and a Professor by Research at Oxford University. He has worked on physical mapping with Hans Lehrach at Imperial Cancer Research Fund laboratories in London, where he developed a suite of software tools for the construction and validation of physical maps In 1995 he moved to the Sanger Centre to work on DNA sequence assembly where he wrote software that automatically analysed sequencing trace data in order to edit DNA sequence assemblies. This was used extensively to accelerate sequence production. He wrote the sequence CAFtools assembly pipeline which was used for the pipeline assembly of the human and other genomes at Sanger, and developed software for spliced alignment of EST to genomic DNA. Between 1999 and 2015 he worked at the Wellcome Trust Ce ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Washington University In St
Washington commonly refers to: * Washington (state), United States * Washington, D.C., the capital of the United States ** A metonym for the federal government of the United States ** Washington metropolitan area, the metropolitan area centered on Washington, D.C. * George Washington George Washington (February 22, 1732, 1799) was an American military officer, statesman, and Founding Father who served as the first president of the United States from 1789 to 1797. Appointed by the Continental Congress as commander of th ... (1732–1799), the first president of the United States Washington may also refer to: Places England * Washington, Tyne and Wear, a town in the City of Sunderland metropolitan borough ** Washington Old Hall, ancestral home of the family of George Washington * Washington, West Sussex, a village and civil parish Greenland * Cape Washington, Greenland * Washington Land Philippines *New Washington, Aklan, a municipality *Washington, a barangay in Catar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Software
Software is a set of computer programs and associated documentation and data. This is in contrast to hardware, from which the system is built and which actually performs the work. At the lowest programming level, executable code consists of machine language instructions supported by an individual processor—typically a central processing unit (CPU) or a graphics processing unit (GPU). Machine language consists of groups of binary values signifying processor instructions that change the state of the computer from its preceding state. For example, an instruction may change the value stored in a particular storage location in the computer—an effect that is not directly observable to the user. An instruction may also invoke one of many input or output operations, for example displaying some text on a computer screen; causing state changes which should be visible to the user. The processor executes the instructions in the order they are provided, unless it is instructed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biology
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary information encoded in genes, which can be transmitted to future generations. Another major theme is evolution, which explains the unity and diversity of life. Energy processing is also important to life as it allows organisms to move, grow, and reproduce. Finally, all organisms are able to regulate their own internal environments. Biologists are able to study life at multiple levels of organization, from the molecular biology of a cell to the anatomy and physiology of plants and animals, and evolution of populations.Based on definition from: Hence, there are multiple subdisciplines within biology, each defined by the nature of their research questions and the tools that they use. Like other scientists, biologists use the sc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular
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 (molecule), 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 typic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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