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Pfam Logo
Pfam is a database of Protein family, protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The latest version of Pfam, 37.0, was released in June 2024 and contains 21,979 families. It is currently provided through InterPro website. Uses The general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. Originally, the rationale behind creating the database was to have a semi-automated method of curating information on known protein families to improve the efficiency of annotating genomes. The Pfam classification of protein families has been widely adopted by biologists because of its wide coverage of proteins and sensible naming conventions. It is used by experimental biologists researching specific proteins, by structural biologists to identify new targets for structure determination, by computational biologists to organise sequences and by evolution ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Domains Of Unknown Function
A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs. The DUF designation is tentative, and such families tend to be renamed to a more specific name (or merged to an existing domain) after a function is identified. History The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database. These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively. Characterisation Structura ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fox Chase Cancer Center
Fox Chase Cancer Center is a National Cancer Institute-designated Comprehensive Cancer Center research facility and hospital located in the Fox Chase section of Philadelphia, Pennsylvania, United States. The main facilities of the center are located on property adjoining Burholme Park. The center is part of the Temple University Health System (TUHS) and specializes in the treatment and prevention of cancer. History The center was formed in 1974 by the merger of the American Oncologic Hospital, which was founded in 1904 as the first cancer hospital in the United States, and the Institute for Cancer Research, founded in 1927. In 1967 a large wing of the hospital was constructed based on a design by Vincent G. Kling using steep slopes of poured concrete and roof tiles by Ludowici. In 1995, Fox Chase also became a founding member of the National Comprehensive Cancer Network, an alliance of 21 of the nation's leading academic cancer centers. The center was an independent, no ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TrEMBL
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, USA. The UniProt consortium The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation (NBRF) at the Georgetown U ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PANDIT (database)
PANDIT is a database of multiple sequence alignments and phylogenetic trees covering many common protein domains. See also * Pfam: database of protein domains * Phylogeny * Sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ... References External links * http://www.ebi.ac.uk/goldman-srv/pandit Biological databases Computational phylogenetics Genetics in the United Kingdom Protein domains Science and technology in Cambridgeshire South Cambridgeshire District {{Biodatabase-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Biological Databases
Biological databases are stores of biological information. The journal ''Nucleic Acids Research'' regularly publishes special issues on biological databases and has a list of such databases. The 2018 issue has a list of about 180 such databases and updates to previously described databasesOmics Discovery Indexcan be used to browse and search several biological databases. Furthermore, thNIAID Data Ecosystem Discovery Portaldeveloped by the National Institute of Allergy and Infectious Diseases (NIAID) enables searching across databases. Meta databases Meta databases are databases of databases that collect data about data to generate new data. They are capable of merging information from different sources and making it available in a new and more convenient form, or with an emphasis on a particular disease or organism. Originally, metadata was only a common term referring simply to ''data about data '' such as tags, keywords, and markup headers. * ConsensusPathDB: a molecular funct ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Zinc Finger
A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. The term ''zinc finger'' was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (''Xenopus laevis'') transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. '' Xenopus laevis'' TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in ''Drosophila''. It often appears as a metal-binding domain in multi-domain proteins. Proteins that contain zinc fingers (zinc finger proteins) are classified into several different structural families. Unlike many other clearly defined supersecondary structures such as Greek keys or β hairpins, ... [...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] |
Rfam
Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families. Unlike proteins, ncRNAs often have similar secondary structure without sharing much similarity in the primary sequence. Rfam divides ncRNAs into families based on evolution from a common ancestor. Producing multiple sequence alignments (MSA) of these families can provide insight into their structure and function, similar to the case of protein families. These MSAs become more useful with the addition of secondary structure information. Rfam researchers also contribute to Wikipedia's RNA WikiProject. Uses The Rfam database can be used for a variety of functions. For each ncRNA fa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Website
A website (also written as a web site) is any web page whose content is identified by a common domain name and is published on at least one web server. Websites are typically dedicated to a particular topic or purpose, such as news, education, commerce, entertainment, or social media. Hyperlinking between web pages guides the navigation of the site, which often starts with a home page. The most-visited sites are Google, YouTube, and Facebook. All publicly-accessible websites collectively constitute the World Wide Web. There are also private websites that can only be accessed on a private network, such as a company's internal website for its employees. Users can access websites on a range of devices, including desktops, laptops, tablets, and smartphones. The app used on these devices is called a web browser. Background The World Wide Web (WWW) was created in 1989 by the British CERN computer scientist Tim Berners-Lee. On 30 April 1993, CERN announced that the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Clans
A clan is a group of people united by actual or perceived kinship and descent. Even if lineage details are unknown, a clan may claim descent from a founding member or apical ancestor who serves as a symbol of the clan's unity. Many societies' exogamy rules are on a clan basis, where all members of one's own clan, or the clans of both parents or even grandparents, are excluded from marriage as incest. Clans preceded more centralized forms of community organization and government, and have existed in every country. Members may identify with a coat of arms or other symbol. Etymology The word "clan" is derived from the Gaelic word meaning "children", "offspring", "progeny" or "descendants". According to the ''Oxford English Dictionary'', the word "clan" was introduced into English in around 1406, as a descriptive label for the organization of society in Ireland and the Scottish Highlands. None of the Irish and Scottish Gaelic terms for kinship groups is cognate to English ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Caenorhabditis Elegans
''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a Hybrid word, blend of the Greek ''caeno-'' (recent), ''rhabditis'' (rod-like) and Latin ''elegans'' (elegant). In 1900, Émile Maupas, Maupas initially named it ''Rhabditidae, Rhabditides elegans.'' Günther Osche, Osche placed it in the subgenus ''Caenorhabditis'' in 1952, and in 1955, Ellsworth Dougherty, Dougherty raised ''Caenorhabditis'' to the status of genus. ''C. elegans'' is an unsegmented pseudocoelomate and lacks respiratory or circulatory systems. Most of these nematodes are hermaphrodites and a few are males. Males have specialised tails for mating that include spicule (nematode), spicules. In 1963, Sydney Brenner proposed research into ''C. elegans,'' primarily in the area of neuronal development. In 1974, he began research into the molecular biology, molecular and developmental ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
