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Orthologous MAtrix
OMA (Orthologous MAtrix) is a database of orthologs extracted from available complete genomes. The orthology predictions of OMA are available in several forms: * OMA Pairs: for a given gene, a list of predicted orthologs in other species is provided. * OMA Groups: a set of genes across different species which are all orthologous. * OMA Hierarchical Groups: the set of all genes that have evolved from a single ancestral gene in a given taxonomic range. * OMA Genome Pair view: the list of all predicted orthologs between two species. See also * Homology (biology) * OrthoDB * TreeFam TreeFam (Tree families database) is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. ... References Genetics databases Evolutionary biology Phylogenetics {{Biodatabase-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance. A database management system (DBMS) is the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS software additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Homology (biology)
In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of primates, the front flippers of whales and the forelegs of four-legged vertebrates like dogs and crocodiles are all derived from the same ancestral tetrapod structure. Evolutionary biology explains homologous structures adapted to different purposes as the result of descent with modification from a common ancestor. The term was first applied to biology in a non-evolutionary context by the anatomist Richard Owen in 1843. Homology was later explained by Charles Darwin's theory of evolution in 1859, but had been observed before this, from Aristotle onwards, and it was explicitly analysed by Pierre Belon in 1555. In developmental biology, organs that developed in the embryo in the same manner and from similar origins, such as from matching p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ETH Zurich
(colloquially) , former_name = eidgenössische polytechnische Schule , image = ETHZ.JPG , image_size = , established = , type = Public , budget = CHF 1.896 billion (2021) , rector = Günther Dissertori , president = Joël Mesot , academic_staff = 6,612 (including doctoral students, excluding 527 professors of all ranks, 34% female, 65% foreign nationals) (full-time equivalents 2021) , administrative_staff = 3,106 (40% female, 19% foreign nationals, full-time equivalents 2021) , students = 24,534 (headcount 2021, 33.3% female, 37% foreign nationals) , undergrad = 10,642 , postgrad = 8,299 , doctoral = 4,460 , other = 1,133 , address = Rämistrasse 101CH-8092 ZürichSwitzerland , city = Zürich , coor = , campus = Urban , language = German, English (Masters and upwards, sometimes Bachelor) , affiliations = CESAER, EUA, GlobalTech, IARU, IDEA League, UNITECH , website ethz.ch, colors = Black and White , logo = ETH Zürich Logo black.svg ETH Züric ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Christophe Dessimoz
Christophe Dessimoz is a Swiss National Science Foundation (SNSF) Professor at the University of Lausanne, Associate Professor at University College London and a group leader at the Swiss Institute of Bioinformatics. He was awarded the Overton Prize in 2019 for his contributions to computational biology. Starting in April 2022, he will be joint executive director of the SIB Swiss Institute of Bioinformatics, along with Ron Appel. Education Dessimoz obtained his Master of Science degree in 2003 and PhD in Computer Science in 2009 from ETH Zurich in Switzerland where his doctoral research was supervised by Gaston Gonnet and examined by Amos Bairoch. Career and research After postdoctoral research at the European Bioinformatics Institute (EBI) on the Wellcome Genome Campus in Hinxton, Cambridgeshire, he joined University College London (UCL) as lecturer in 2013, and was promoted to Reader (academic rank), Reader in 2015. In 2015, he joined the University of Lausanne as professo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gaston Gonnet
Gaston H. Gonnet is a Uruguayan Canadian computer scientist and entrepreneur. He is best known for his contributions to the Maple computer algebra system and the creation of a digital version of the Oxford English Dictionary. Education and early life Gonnet received his doctorate in computer science from the University of Waterloo in 1977. His thesis was entitled ''Interpolation and Interpolation-Hash Searching''. His advisor was J. Alan George. Career and research In 1980 Gonnet co-founded the Symbolic Computation Group at the University of Waterloo. The work of SCG on a general-purpose computer algebra system later formed the core of the Maple system. In 1988, Gonnet co-founded (with Keith Geddes) the private company Waterloo Maple Inc., to sell Maple commercially. In the mid 1990s the company ran into trouble and a disagreement between his colleagues caused him to withdraw from chairman of the Board and managerial involvement. In 1984 Gonnet co-founded the New Oxford ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genome Sequencing
Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. Whole genome sequencing has largely been used as a research tool, but was being introduced to clinics in 2014. In the future of personalized medicine, whole genome sequence data may be an important tool to guide therapeutic intervention. The tool of gene sequencing at SNP level is also used to pinpoint functional variants from association studies and improve the knowledge available to researchers interested in evolutionary biology, and hence may lay the foundation for predicting disease susceptibility and drug response. Whole genome sequencing should not be confused with DNA profil ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined. The most recent rigorous estimate for the total number of species of eukaryotes is between 8 and 8.7 million. However, only about 14% of these had been described by 2011. All species (except viruses) are given a two-part name, a "binomial". The first part of a binomial is the genus to which the species belongs. The second part is called the specific name or the specific epithet (in botanical nomenclature, also sometimes i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Taxonomy (biology)
In biology, taxonomy () is the scientific study of naming, defining ( circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (''division'' is sometimes used in botany in place of ''phylum''), class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms. With advances in the theory, data and analytical technology of biological systematics, the Linnaean system has transformed into a system of modern biological classification intended to reflect the evolu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OrthoDB
OrthoDB presents a catalog of orthologous protein-coding genes across vertebrates, arthropods, fungi, plants, and bacteria. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each major radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive orthology database querying. OrthoDB also provides computed evolutionary traits of orthologs, such as gene duplicability and loss profiles, divergence rates, sibling groups, and gene intron-exon architectures. In comparative genomics, the importance of scale cannot be underestimated. As gene orthology delineation requires specific expertise and considerable computational resources, scale is something that individual non-specialist research groups cannot ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TreeFam
TreeFam (Tree families database) is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (''S.cerevisiae'' and ''S. pombe'') and plant (''A. thaliana'') to reveal these distant members. TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations. The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetics Databases
Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar working in the 19th century in Brno, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene. Trait inheritance and molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded to study the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the cell, the organism (e.g. dominance), and within the context o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
