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Mutalyzer
Mutalyzer is a web-based software tool which was primarily developed to check the description of mutation, sequence variants identified in a gene during genetic testing. Mutalyzer applies the rules of the standard human sequence variant nomenclature and can correct descriptions accordingly. Apart from the sequence variant description, Mutalyzer requires a DNA sequence record containing the MRNA, transcript and protein feature annotation as a reference. Mutalyzer 2 accepts GenBank and Locus Reference Genomic (LRG) records. The annotation is also used to apply the correct Genetic code, codon translation tables and generate DNA and protein variant descriptions for any organism. The Mutalyzer server supports programmatic access via a SOAP Web service described in the Web Services Description Language (WSDL) and an HTTP/Remote procedure call, RPC+JSON web service. Background Genetic testing is generally performed in families with Genetic disorder, hereditary disease. Any sequence varian ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mutation
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA replication, DNA or viral replication, mitosis, or meiosis or other types of DNA repair#DNA damage, damage to DNA (such as pyrimidine dimers caused by exposure to ultraviolet radiation), which then may undergo error-prone repair (especially microhomology-mediated end joining), cause an error during other forms of repair, or cause an error during replication (DNA repair#Translesion synthesis, translesion synthesis). Mutations may also result from Insertion (genetics), insertion or Deletion (genetics), deletion of segments of DNA due to mobile genetic elements. Mutations may or may not produce detectable changes in the observable characteristics (phenotype) of an organism. Mutations play a part in both normal and abnormal biological processes including: evolution, cancer ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LOVD
The Leiden Open Variation Database (LOVD) is a free, flexible web-based open source database developed in the Leiden University Medical Center in the Netherlands, designed to collect and display variants in the DNA sequence. The focus of an LOVD is usually the combination between a gene and a genetic (heritable) disease. All sequence variants found in individuals are collected in the database, together with information about whether they could be causally connected to the disease (i.e. a disease-causing variant or mutation) or not (i.e. a non-disease causing variant). Specialized doctors (clinical geneticists) use LOVDs to diagnose and advise patients carrying a genetic disease. Ideally, if a patient has been screened for mutations and one has been found, information in LOVD can predict the progress of the disease. In contrast to human genome databases, showing information on all DNA variants, LOVDs include information about the individuals in which the variants were found. This p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Locus Reference Genomic
Locus Reference Genomic (LRG) is a DNA sequence format that was developed to aid in curating locus specific databases (LSDBs) that record DNA sequence variation which can result in inherited diseases. LRGs have fixed sequences that are independent of the genome so that they provide a stable framework for reporting variants. The LRG format uses extensible markup language (XML) to provide highly structured single records containing the genomic DNA sequence for individual genes along with the mRNAs and proteins encoded by these genes. LRG records are recommended in thHuman Genome Variation Society Nomenclature guidelinesas reference sequences to report sequence variants in LSDBs and the literature. The LRG concept was developed by thGEN2PHEN projectin conjunction with the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine ( ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Remote Procedure Call
In distributed computing, a remote procedure call (RPC) is when a computer program causes a procedure ( subroutine) to execute in a different address space (commonly on another computer on a shared network), which is coded as if it were a normal (local) procedure call, without the programmer explicitly coding the details for the remote interaction. That is, the programmer writes essentially the same code whether the subroutine is local to the executing program, or remote. This is a form of client–server interaction (caller is client, executor is server), typically implemented via a request–response message-passing system. In the object-oriented programming paradigm, RPCs are represented by remote method invocation (RMI). The RPC model implies a level of location transparency, namely that calling procedures are largely the same whether they are local or remote, but usually, they are not identical, so local calls can be distinguished from remote calls. Remote calls are usually ord ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ensembl
Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information. Similar databases and browsers are found at NCBI and the University of California, Santa Cruz (UCSC). History The human genome consists of three billion base pairs, which code for approximately 20,000–25,000 genes. However the genome alone is of little use, unless the locations and relationships of individual genes can be identified. One option is manual annotation, whereby a team of scientists tries to locate genes using experimental data from scientific journals and public databases. However this is a slow, painstaking task. The alternative, known as automated annotation, is to use the power of computers ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Guanine
Guanine () ( symbol G or Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine (uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is called guanosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine- imidazole ring system with conjugated double bonds. This unsaturated arrangement means the bicyclic molecule is planar. Properties Guanine, along with adenine and cytosine, is present in both DNA and RNA, whereas thymine is usually seen only in DNA, and uracil only in RNA. Guanine has two tautomeric forms, the major keto form (see figures) and rare enol form. It binds to cytosine through three hydrogen bonds. In cytosine, the amino group acts as the hydrogen bond donor and the C-2 carbonyl and the N-3 amine as the hydrogen-bond acceptors. Guanine has the C-6 carbonyl group that acts as the hydrogen bond acceptor, while a g ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha amino acids appear in the genetic code. Amino acids can be classified according to the locations of the core structural functional groups, as Alpha and beta carbon, alpha- , beta- , gamma- or delta- amino acids; other categories relate to Chemical polarity, polarity, ionization, and side chain group type (aliphatic, Open-chain compound, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid '' residues'' form the second-largest component (water being the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. It is thought that they played a key role in enabling l ... [...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] |
Genetic Disorder
A genetic disorder is a health problem caused by one or more abnormalities in the genome. It can be caused by a mutation in a single gene (monogenic) or multiple genes (polygenic) or by a chromosomal abnormality. Although polygenic disorders are the most common, the term is mostly used when discussing disorders with a single genetic cause, either in a gene or chromosome. The mutation responsible can occur spontaneously before embryonic development (a ''de novo'' mutation), or it can be inherited from two parents who are carriers of a faulty gene (autosomal recessive inheritance) or from a parent with the disorder (autosomal dominant inheritance). When the genetic disorder is inherited from one or both parents, it is also classified as a hereditary disease. Some disorders are caused by a mutation on the X chromosome and have X-linked inheritance. Very few disorders are inherited on the Y chromosome or mitochondrial DNA (due to their size). There are well over 6,000 known genet ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetic Testing
Genetic testing, also known as DNA testing, is used to identify changes in DNA sequence or chromosome structure. Genetic testing can also include measuring the results of genetic changes, such as RNA analysis as an output of gene expression, or through biochemical analysis to measure specific protein output. In a medical setting, genetic testing can be used to diagnose or rule out suspected genetic disorders, predict risks for specific conditions, or gain information that can be used to customize medical treatments based on an individual's genetic makeup. Genetic testing can also be used to determine biological relatives, such as a child's biological parentage (genetic mother and father) through DNA paternity testing, or be used to broadly predict an individual's ancestry. Genetic testing of plants and animals can be used for similar reasons as in humans (e.g. to assess relatedness/ancestry or predict/diagnose genetic disorders), to gain information used for selective breedin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JSON
JSON (JavaScript Object Notation, pronounced ; also ) is an open standard file format and data interchange format that uses human-readable text to store and transmit data objects consisting of attribute–value pairs and arrays (or other serializable values). It is a common data format with diverse uses in electronic data interchange, including that of web applications with servers. JSON is a language-independent data format. It was derived from JavaScript, but many modern programming languages include code to generate and parse JSON-format data. JSON filenames use the extension .json. Any valid JSON file is a valid JavaScript (.js) file, even though it makes no changes to a web page on its own. Douglas Crockford originally specified the JSON format in the early 2000s. He and Chip Morningstar sent the first JSON message in April 2001. Naming and pronunciation The 2017 international standard (ECMA-404 and ISO/IEC 21778:2017) specifies "Pronounced , as in ' Jason and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Web Services Description Language
The Web Services Description Language (WSDL ) is an XML-based interface description language that is used for describing the functionality offered by a web service. The acronym is also used for any specific WSDL description of a web service (also referred to as a ''WSDL file''), which provides a machine-readable description of how the service can be called, what parameters it expects, and what data structures it returns. Therefore, its purpose is roughly similar to that of a type signature in a programming language. The latest version of WSDL, which became a W3C recommendation in 2007, is WSDL 2.0. The meaning of the acronym has changed from version 1.1 where the "D" stood for "Definition". Description The WSDL describes services as collections of network endpoints, or ports. The WSDL specification provides an XML format for documents for this purpose. The abstract definitions of ports and messages are separated from their concrete use or instance, allowing the reuse of the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
