|
Phred Quality Score
A Phred quality score is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing. It was originally developed for the computer program Phred (software), Phred to help in the automation of DNA sequencing in the Human Genome Project. Phred quality scores are assigned to each nucleotide base call in automated sequencer traces. The FASTQ format encodes phred scores as ASCII characters alongside the read sequences. 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. Perhaps the most important use of Phred quality scores is the automatic determination of accurate, quality-based consensus sequences. Definition Phred quality scores Q are logarithmically related to the base-calling error probabilities P and defined as Q = -10 \ \log_ P. This relation can be also be written as P = 10^. For example, if Phred assigns a quali ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phred Figure 1
Phred may refer to: *Phred (software), a computer program used in molecular biology *Phred quality score, a term used in molecular biology *Phred (Doonesbury), a character from the comic strip Doonesbury *Phred on Your Head Show, a children's television show *The URL with Phred Show, a spin-off of the above See also *Fred (other) {{disambig ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phred Base Calling
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 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 CCD on the DNA sequencer and this produces a time "trace" data (or "chr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Moving Picture Experts Group
The Moving Picture Experts Group (MPEG) is an alliance of working groups established jointly by ISO and IEC that sets standards for media coding, including compression coding of audio, video, graphics, and genomic data; and transmission and file formats for various applications.John Watkinson, ''The MPEG Handbook'', p. 1 Together with JPEG, MPEG is organized under ISO/IEC JTC 1/SC 29 – ''Coding of audio, picture, multimedia and hypermedia information'' (ISO/IEC Joint Technical Committee 1, Subcommittee 29). MPEG formats are used in various multimedia systems. The most well known older MPEG media formats typically use MPEG-1, MPEG-2, and MPEG-4 AVC media coding and MPEG-2 systems transport streams and program streams. Newer systems typically use the MPEG base media file format and dynamic streaming (a.k.a. MPEG-DASH). History MPEG was established in 1988 by the initiative of Dr. Hiroshi Yasuda ( NTT) and Dr. Leonardo Chiariglione (CSELT). Chiariglione was the group' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lossy Compression
In information technology, lossy compression or irreversible compression is the class of data compression methods that uses inexact approximations and partial data discarding to represent the content. These techniques are used to reduce data size for storing, handling, and transmitting content. The different versions of the photo of the cat on this page show how higher degrees of approximation create coarser images as more details are removed. This is opposed to lossless data compression (reversible data compression) which does not degrade the data. The amount of data reduction possible using lossy compression is much higher than using lossless techniques. Well-designed lossy compression technology often reduces file sizes significantly before degradation is noticed by the end-user. Even when noticeable by the user, further data reduction may be desirable (e.g., for real-time communication or to reduce transmission times or storage needs). The most widely used lossy compression al ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lossless Compression
Lossless compression is a class of data compression that allows the original data to be perfectly reconstructed from the compressed data with no loss of information. Lossless compression is possible because most real-world data exhibits statistical redundancy. By contrast, lossy compression permits reconstruction only of an approximation of the original data, though usually with greatly improved compression rates (and therefore reduced media sizes). By operation of the pigeonhole principle, no lossless compression algorithm can efficiently compress all possible data. For this reason, many different algorithms exist that are designed either with a specific type of input data in mind or with specific assumptions about what kinds of redundancy the uncompressed data are likely to contain. Therefore, compression ratios tend to be stronger on human- and machine-readable documents and code in comparison to entropic binary data (random bytes). Lossless data compression is used in many ... [...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] |
Gene Codes Corporation
Gene Codes Corporation is a privately owned international firm based in Ann Arbor, Michigan, which specializes in bioinformatics software for genetic sequence analysis. Its flagship software product, Sequencher, is a sequencing software used throughout the world. Its targeted use is by researchers at academic and government labs as well as biotechnology and pharmaceutical companies for DNA sequence assembly. History Gene Codes Corporation was founded in 1988 in Ann Arbor, Michigan. In 1991, the DNA sequence assembly and analysis software, Sequencher, was released. By 1997, nearly every major pharmaceutical company and commercial genomics company in the world was standardized on Sequencher, as well as the majority of labs at major academic centers. Sequencher 5.4 was released in 2015. [...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] |
Applied Biosystems
Applied Biosystems is one of various brands under the Life Technologies brand of Thermo Fisher Scientific corporation. The brand is focused on integrated systems for genetic analysis, which include computerized machines and the consumables used within them (such as reagents). In 2008, a merger between Applied Biosystems and Invitrogen was finalized, creating Life Technologies. The latter was acquired by Thermo Fisher Scientific in 2014. Prior to 2008, the Applied Biosystems brand was owned by various entities in a corporate group parented by PerkinElmer. The roots of Applied Biosystems trace back to GeneCo (Genetic Systems Company), a pioneer biotechnology company founded in 1981 in Foster City, California.Applied Biosystems Timeline , AppliedBiosystems.com Through the 1980s and early 199 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LI-COR Biosciences
LI-COR Biosciences is an international biotech company which designs, manufactures, and markets instruments, measurement systems, and software for biological and environmental research, and develops relevant measurement methodologies and techniques. Origins and history LI-COR Biosciences was a privately held company based in Lincoln, Nebraska, until its acquisition by Battery Ventures in 2021. It was founded in 1971 under the name Lambda Instruments Corporation. The name was shortened to LI-COR, Inc., in 1978. Products and Applications Biotechnology LI-COR biotechnology instruments, software and reagents, which are based on near-infrared fluorescent and chemiluminescent detection, are used in a large variety of assays, such as western blot assays and cell-based assays, as well as ''in vivo'' imaging and DNA analysis. Primary applications include cancer research, drug discovery, genomics research, neuroscience, cell biology, and education. Environmental LI-COR environmental i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Michael Waterman
Michael Spencer Waterman (born June 28, 1942) is a Professor of Biology, Mathematics and Computer Science at the University of Southern California (USC), where he holds an Endowed Associates Chair in Biological Sciences, Mathematics and Computer Science. He previously held positions at Los Alamos National Laboratory and Idaho State University. Education and early life Waterman grew up near Bandon, Oregon, and earned a bachelor's degree in Mathematics from Oregon State University, followed by a PhD in statistics and probability from Michigan State University in 1969. Research and career Waterman is one of the founders and current leaders in the area of computational biology. He focuses on applying mathematics, statistics, and computer science techniques to various problems in molecular biology. His work has contributed to some of the most widely used tools in the field. In particular, the Smith-Waterman algorithm (developed with Temple F. Smith) is the basis for many sequence al ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleobase
Nucleobases, also known as ''nitrogenous bases'' or often simply ''bases'', are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases—adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called ''primary'' or ''canonical''. They function as the fundamental units of the genetic code, with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA. Thymine and uracil are distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings. In addition, some viruses have aminoadenine (Z) instead of adenine. It differs in having an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
