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Newbler
Newbler is a software package for '' de novo'' DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Sciences, a Roche Diagnostics company. Usage Newbler can run via a Java GUI (gsAssembler) or the command line (runAssembly). It works natively with the .SFF data output by the sequencer, but is also able to accept FASTA files, containing nucleotide sequences, with or without quality information, and FASTQ files. It will use older Sanger sequence data if appropriately formatted to aid in assembly and scaffolding. See also *Sequencing *Sequence assembly In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one ... References External links454 Sequencing home page Bioinformatics software ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Assembly
In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used. Typically, the short fragments (reads) result from shotgun sequencing genomic DNA, or gene transcript ( ESTs). The problem of sequence assembly can be compared to taking many copies of a book, passing each of them through a shredder with a different cutter, and piecing the text of the book back together just by looking at the shredded pieces. Besides the obvious difficulty of this task, there are some extra practical issues: the original may have many repeated paragraphs, and some shreds may be modified during shredding to have typos. Excerpts from another book may also be added in, and some shreds may be completely unrecognizable. Genom ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Assembly
In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used. Typically, the short fragments (reads) result from shotgun sequencing genomic DNA, or gene transcript ( ESTs). The problem of sequence assembly can be compared to taking many copies of a book, passing each of them through a shredder with a different cutter, and piecing the text of the book back together just by looking at the shredded pieces. Besides the obvious difficulty of this task, there are some extra practical issues: the original may have many repeated paragraphs, and some shreds may be modified during shredding to have typos. Excerpts from another book may also be added in, and some shreds may be completely unrecognizable. Genom ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
454 Life Sciences
454 Life Sciences was a biotechnology company based in Branford, Connecticut that specialized in high-throughput DNA sequencing. It was acquired by Roche in 2007 and shut down by Roche in 2013 when its technology became noncompetitive, although production continued until mid-2016. History 454 Life Sciences was founded by Jonathan Rothberg and was originally known as 454 Corporation, a subsidiary of CuraGen. For their method for low-cost gene sequencing, 454 Life Sciences was awarded the Wall Street Journal's Gold Medal for Innovation in the Biotech-Medical category in 2005. The name 454 was the code name by which the project was referred to at CuraGen, and the numbers have no known special meaning. In November 2006, Rothberg, Michael Egholm, and colleagues at 454 published a cover article with Svante Pääbo in Nature describing the first million base pairs of the Neanderthal genome, and initiated the Neanderthal Genome Project to complete the sequence of the Neanderthal ge ... [...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] |
De Novo Synthesis
In chemistry, ''de novo'' synthesis () refers to the synthesis of complex molecules from simple molecules such as sugars or amino acids, as opposed to recycling after partial degradation. For example, nucleotides are not needed in the diet as they can be constructed from small precursor molecules such as formate and aspartate. Methionine, on the other hand, is needed in the diet because while it can be degraded to and then regenerated from homocysteine, it cannot be synthesized ''de novo''. Nucleotide ''De novo'' pathways of nucleotides do not use free bases: adenine (abbreviated as A), guanine (G), cytosine (C), thymine (T), or uracil (U). The purine ring is built up one atom or a few atoms at a time and attached to ribose throughout the process. Pyrimidine ring is synthesized as orotate and attached to ribose phosphate and later converted to common pyrimidine nucleotides. Cholesterol Cholesterol is an essential structural component of animal cell membranes. Cholestero ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pyrosequencing
Pyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle, in which the sequencing is performed by detecting the nucleotide incorporated by a DNA polymerase. Pyrosequencing relies on light detection based on a chain reaction when pyrophosphate is released. Hence, the name pyrosequencing. The principle of pyrosequencing was first described in 1993 by, Bertil Pettersson, Mathias Uhlen and Pål Nyren by combining the solid phase sequencing method using streptavidin coated magnetic beads with recombinant DNA polymerase lacking 3´to 5´exonuclease activity (proof-reading) and luminescence detection using the firefly luciferase enzyme. A mixture of three enzymes (DNA polymerase, ATP sulfurylase and firefly luciferase) and a nucleotide (dNTP) are added to single stranded DNA to be sequenced and the incorporation of nucleotide is followed by measuring the light emitted. The intensity of the light determi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Roche Diagnostics
F. Hoffmann-La Roche AG, commonly known as Roche, is a Swiss multinational healthcare company that operates worldwide under two divisions: Pharmaceuticals and Diagnostics. Its holding company, Roche Holding AG, has shares listed on the SIX Swiss Exchange. The company headquarters are located in Basel. Roche is the fifth largest pharmaceutical company in the world by revenue, and the leading provider of cancer treatments globally. The company controls the American biotechnology company Genentech, which is a wholly owned affiliate, and the Japanese biotechnology company Chugai Pharmaceuticals, as well as the United States-based companies Ventana and Foundation Medicine. Roche's revenues during fiscal year 2020 were 58.32 billion Swiss francs. Descendants of the founding Hoffmann and Oeri families own slightly over half of the bearer shares with voting rights (a pool of family shareholders 45%, and Maja Oeri a further 5% apart), with Swiss pharma firm Novartis owning a further ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java (software Platform)
Java is a set of computer software and specifications developed by James Gosling at Sun Microsystems, which was later acquired by the Oracle Corporation, that provides a system for developing application software and deploying it in a cross-platform computing environment. Java is used in a wide variety of computing platforms from embedded devices and mobile phones to enterprise servers and supercomputers. Java applets, which are less common than standalone Java applications, were commonly run in secure, sandboxed environments to provide many features of native applications through being embedded in HTML pages. Writing in the Java programming language is the primary way to produce code that will be deployed as byte code in a Java virtual machine (JVM); byte code compilers are also available for other languages, including Ada, JavaScript, Python, and Ruby. In addition, several languages have been designed to run natively on the JVM, including Clojure, Groovy, and Scala. J ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Command Line
A command-line interpreter or command-line processor uses a command-line interface (CLI) to receive commands from a user in the form of lines of text. This provides a means of setting parameters for the environment, invoking executables and providing information to them as to what actions they are to perform. In some cases the invocation is conditional based on conditions established by the user or previous executables. Such access was first provided by computer terminals starting in the mid-1960s. This provided an interactive environment not available with punched cards or other input methods. Today, many users rely upon graphical user interfaces and menu-driven interactions. However, some programming and maintenance tasks may not have a graphical user interface and use a command line. Alternatives to the command-line interface include text-based user interface menus (for example, IBM AIX SMIT), keyboard shortcuts, and various desktop metaphors centered on the pointer (usual ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA Format
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics. The simplicity of FASTA format makes it easy to manipulate and parse sequences using text-processing tools and scripting languages like the R programming language, Python, Ruby, Haskell, and Perl. Original format & overview The original FASTA/Pearson format is described in the documentation for the FASTA suite of programs. It can be downloaded with any free distribution of FASTA (see fasta20.doc, fastaVN.doc or fastaVN.me—where VN is the Version Number). In the original format, a sequence was represented as a series of lines, each of whic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fastq
FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity. It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA formatted sequence and its quality data, but has recently become the ''de facto'' standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer. Format A FASTQ file has four line-separated fields per sequence: * Field 1 begins with a '@' character and is followed by a sequence identifier and an ''optional'' description (like a FASTA title line). * Field 2 is the raw sequence letters. * Field 3 begins with a '+' character and is ''optionally'' followed by the same sequence identifier (and any description) again. * Field 4 encodes the quality values for the sequence in Field 2, and must contain the same num ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequencing
In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succinctly summarizes much of the atomic-level structure of the sequenced molecule. DNA sequencing DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. So far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as pyrosequencing are gaining an increasing share of the sequencing market. More genome data are now being produced by pyrosequencing than Sanger DNA sequencing. Pyrosequencing has enabled rapid genome sequencing. Bacterial genomes can be sequenced in a single run with several times cover ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
