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GLIMMER
In bioinformatics, GLIMMER (Gene Locator and Interpolated Markov ModelER) is used to find genes in prokaryotic DNA. "It is effective at finding genes in bacteria, archea, viruses, typically finding 98-99% of all relatively long protein coding genes". GLIMMER was the first system that used the interpolated Markov model to identify coding regions. The GLIMMER software is open source and is maintained by Steven Salzberg, Art Delcher, and their colleagues at the ''Center for Computational Biology'' at Johns Hopkins University. The original GLIMMER algorithms and software were designed by Art Delcher, Simon Kasif and Steven Salzberg and applied to bacterial genome annotation in collaboration with Owen White. Versions GLIMMER 1.0 First Version of GLIMMER "i.e., GLIMMER 1.0" was released in 1998 and it was published in the paper ''Microbial gene identification using interpolated Markov model''. Markov models were used to identify microbial genes in GLIMMER 1.0. GLIMMER considers the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Owen White
Owen White is a bioinformatician and director of the Institute For Genome Sciences at the University of Maryland School of Medicine. He is known for his work on the bioinformatics tools GLIMMER and MUMmer. Education White studied biotechnology at the University of Massachusetts Amherst, gaining a bachelor of science degree in 1985. He later studied with Christopher A. Fields at New Mexico State University, gaining his PhD in molecular biology in 1992. Research From 1992 to 1994, White was a postdoctoral fellow in the Genome Informatics department at The Institute for Genomic Research (TIGR) in Rockville, Maryland. This was followed by a period as a collaborative investigator in the Department of Bioinformatics at TIGR. While at TIGR, White was one of the developers of the GLIMMER (Gene Locator and Interpolated Markov ModelER) gene discovery algorithm, alongside Steven Salzberg and colleagues. Salzberg and White were also involved in the development of the MUMmer software for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Steven Salzberg
Steven Lloyd Salzberg (born 1960) is an American computational biologist and computer scientist who is a Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics at Johns Hopkins University, where he is also Director of the Center for Computational Biology. Early life and education Salzberg was born in 1960 as one of four children to Herman Salzberg, a Distinguished Professor Emeritus of Psychology, and Adele Salzberg, a retired school teacher. Salzberg did his undergraduate studies at Yale University where he received his Bachelor of Arts degree in English in 1980. In 1981 he returned to Yale, and he received his Master of Science and Master of Philosophy degrees in Computer Science in 1982 and 1984, respectively. After several years in a startup company, he enrolled at Harvard University, where he earned a Ph.D. in Computer Science in 1989. Career After earning his Ph.D., Salzberg joined Johns Hopkins University as an Assistant Professo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Prediction
In computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced. In its earliest days, "gene finding" was based on painstaking experimentation on living cells and organisms. Statistical analysis of the rates of homologous recombination of several different genes could determine their order on a certain chromosome, and information from many such experiments could be combined to create a genetic map specifying the rough location of known genes relative to each other. Today, with comprehensive genome sequence and powerful computational resources at the disposal of the research community, gene finding has been redefined as a largely computatio ... [...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 properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Reading Frame
In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible reading frames will be "open" (the "reading", however, refers to the RNA produced by transcription of the DNA and its subsequent interaction with the ribosome in translation). Such an ORF may contain a start codon (usually AUG in terms of RNA) and by definition cannot extend beyond a stop codon (usually UAA, UAG or UGA in RNA). That start codon (not necessarily the first) indicates where translation may start. The transcription termination site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, an incomplete protein would be made during translation. In eukaryotic genes with multiple exons, introns are removed and exons are then joined together after transcription to yield the final ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Training Set
In machine learning, a common task is the study and construction of algorithms that can learn from and make predictions on data. Such algorithms function by making data-driven predictions or decisions, through building a mathematical model from input data. These input data used to build the model are usually divided in multiple data sets. In particular, three data sets are commonly used in different stages of the creation of the model: training, validation and test sets. The model is initially fit on a training data set, which is a set of examples used to fit the parameters (e.g. weights of connections between neurons in artificial neural networks) of the model. The model (e.g. a naive Bayes classifier) is trained on the training data set using a supervised learning method, for example using optimization methods such as gradient descent or stochastic gradient descent. In practice, the training data set often consists of pairs of an input vector (or scalar) and the corresponding ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Noncoding DNA
Non-coding DNA (ncDNA) sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is transcribed into functional non-coding RNA molecules (e.g. transfer RNA, microRNA, piRNA, ribosomal RNA, and regulatory RNAs). Other functional regions of the non-coding DNA fraction include regulatory sequences that control gene expression; scaffold attachment regions; origins of DNA replication; centromeres; and telomeres. Some non-coding regions appear to be mostly nonfunctional such as introns, pseudogenes, intergenic DNA, and fragments of transposons and viruses. Fraction of non-coding genomic DNA In bacteria, the coding regions typically take up 88 % of the genome. The remaining 12 % consists largely of non-coding genes and regulatory sequences, which means that almost all of the bacterial genome has a function. The amount of coding DNA in eukaryrotes is usually a much smaller fraction of the genome because eukaryotic genomes contai ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
K-mer
In bioinformatics, ''k''-mers are substrings of length k contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which ''k''-mers are composed of nucleotides (''i.e''. A, T, G, and C), ''k''-mers are capitalized upon to assemble DNA sequences, improve heterologous gene expression, identify species in metagenomic samples, and create attenuated vaccines. Usually, the term ''k''-mer refers to all of a sequence's subsequences of length k, such that the sequence AGAT would have four monomers (A, G, A, and T), three 2-mers (AG, GA, AT), two 3-mers (AGA and GAT) and one 4-mer (AGAT). More generally, a sequence of length L will have L - k + 1 ''k''-mers and n^ total possible ''k''-mers, where n is number of possible monomers (e.g. four in the case of DNA). Introduction ''k''-mers are simply length k subsequences. For example, all the possible ''k''-mers of a DNA sequence are shown below: A method of visualizi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Oligomer
In chemistry and biochemistry, an oligomer () is a molecule that consists of a few repeating units which could be derived, actually or conceptually, from smaller molecules, monomers.Quote: ''Oligomer molecule: A molecule of intermediate relative molecular mass, the structure of which essentially comprises a small plurality of units derived, actually or conceptually, from molecules of lower relative molecular mass.'' The name is composed of Greek elements '' oligo-'', "a few" and '' -mer'', "parts". An adjective form is ''oligomeric''. The oligomer concept is contrasted to that of a polymer, which is usually understood to have a large number of units, possibly thousands or millions. However, there is no sharp distinction between these two concepts. One proposed criterion is whether the molecule's properties vary significantly with the removal of one or a few of the units. An oligomer with a specific number of units is referred to by the Greek prefix denoting that number, wi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Case 1
Case or CASE may refer to: Containers * Case (goods), a package of related merchandise * Cartridge case or casing, a firearm cartridge component * Bookcase, a piece of furniture used to store books * Briefcase or attaché case, a narrow box to carry paperwork * Computer case, the enclosure for a PC's main components * Keep case, DVD or CD packaging * Pencil case * Phone case, protective or vanity accessory for mobile phones ** Battery case * Road case or flight case, for fragile equipment in transit * Shipping container or packing case * Suitcase, a large luggage box * Type case, a compartmentalized wooden box for letterpress typesetting Places * Case, Laclede County, Missouri * Case, Warren County, Missouri * Case River, a Kabika tributary in Ontario, Canada * Case Township, Michigan * Case del Conte, Italy People * Case (name), people with the surname (or given name) * Case (singer), American R&B singer-songwriter and producer (Case Woodard) Arts, entertainment, and media * ' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Compiler
In computing, a compiler is a computer program that translates computer code written in one programming language (the ''source'' language) into another language (the ''target'' language). The name "compiler" is primarily used for programs that translate source code from a high-level programming language to a low-level programming language (e.g. assembly language, object code, or machine code) to create an executable program. Compilers: Principles, Techniques, and Tools by Alfred V. Aho, Ravi Sethi, Jeffrey D. Ullman - Second Edition, 2007 There are many different types of compilers which produce output in different useful forms. A ''cross-compiler'' produces code for a different CPU or operating system than the one on which the cross-compiler itself runs. A ''bootstrap compiler'' is often a temporary compiler, used for compiling a more permanent or better optimised compiler for a language. Related software include, a program that translates from a low-level language to a h ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Case2
Case or CASE may refer to: Containers * Case (goods), a package of related merchandise * Cartridge case or casing, a firearm cartridge component * Bookcase, a piece of furniture used to store books * Briefcase or attaché case, a narrow box to carry paperwork * Computer case, the enclosure for a PC's main components * Keep case, DVD or CD packaging * Pencil case * Phone case, protective or vanity accessory for mobile phones ** Battery case * Road case or flight case, for fragile equipment in transit * Shipping container or packing case * Suitcase, a large luggage box * Type case, a compartmentalized wooden box for letterpress typesetting Places * Case, Laclede County, Missouri * Case, Warren County, Missouri * Case River, a Kabika tributary in Ontario, Canada * Case Township, Michigan * Case del Conte, Italy People * Case (name), people with the surname (or given name) * Case (singer), American R&B singer-songwriter and producer (Case Woodard) Arts, entertainment, and media * ' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
