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Sequence Read Archive
The Sequence Read Archive (SRA, previously known as the Short Read Archive) is a bioinformatics database that provides a public repository for DNA sequencing data, especially the "short reads" generated by high-throughput sequencing, which are typically less than 1,000 base pairs in length. The archive is part of the International Nucleotide Sequence Database Collaboration (INSDC), and run as a collaboration between the NCBI, the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ). The archive was established by the National Center for Biotechnology Information (NCBI) in 2007 in order to provide a repository for data produced by RNA-Seq and ChIP-Seq studies as well as large-scale studies including the Human Microbiome Project and the 1000 Genomes Project. Originally called the Short Read Archive, the name was changed in anticipation of future sequencing technologies being able to produce longer sequence reads. The volume of data deposited in the Sequenc ... [...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] |
1000 Genomes Project
The 1000 Genomes Project (abbreviated as 1KGP), launched in January 2008, was an international research effort to establish by far the most detailed catalogue of human genetic variation. Scientists planned to sequence the genomes of at least one thousand anonymous participants from a number of different ethnic groups within the following three years, using newly developed technologies which were faster and less expensive. In 2010, the project finished its pilot phase, which was described in detail in a publication in the journal ''Nature''. In 2012, the sequencing of 1092 genomes was announced in a ''Nature'' publication. In 2015, two papers in ''Nature'' reported results and the completion of the project and opportunities for future research. Many rare variations, restricted to closely related groups, were identified, and eight structural-variation classes were analyzed. The project unites multidisciplinary research teams from institutes around the world, including China, Ita ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetics In The United Kingdom
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 ... [...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] |
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. 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.[metadatabase is a database model for metadata management, global query of independent database, and distributed data processing. The word metadatabase is an addition to the dictionary]. originally ,metadata was only common term referring simply to ''data about data '' such a tags ,keywords, and markup headers. * ConsensusPathDB: a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nature Publishing Group
Nature Portfolio (formerly known as Nature Publishing Group and Nature Research) is a division of the international scientific publishing company Springer Nature that publishes academic journals, magazines, online databases, and services in science and medicine. Nature Research's flagship publication is ''Nature'', a weekly multidisciplinary journal first published in 1869. It also publishes the ''Nature-''titled research journals, ''Nature Reviews'' journals (since 2000), society-owned academic journals, and a range of open access journals, including '' Scientific Reports'' and ''Nature Communications''. Springer Nature also publishes ''Scientific American'' in 16 languages, a magazine intended for the general public. In 2013, prior to the merger with Springer and the creation of Springer Nature, Nature Publishing Group's owner, Holtzbrinck Publishing Group, bought a controlling stake in Frontiers. Before Springer Nature was formed in 2015, Nature Research (as the Nature Publi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Access Journals
Open access (OA) is a set of principles and a range of practices through which research outputs are distributed online, free of access charges or other barriers. With open access strictly defined (according to the 2001 definition), or libre open access, barriers to copying or reuse are also reduced or removed by applying an open license for copyright. The main focus of the open access movement is "peer reviewed research literature". Historically, this has centered mainly on print-based academic journals. Whereas non-open access journals cover publishing costs through access tolls such as subscriptions, site licenses or pay-per-view charges, open-access journals are characterised by funding models which do not require the reader to pay to read the journal's contents, relying instead on author fees or on public funding, subsidies and sponsorships. Open access can be applied to all forms of published research output, including peer-reviewed and non peer-reviewed academic journ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Application Programming Interface
An application programming interface (API) is a way for two or more computer programs to communicate with each other. It is a type of software interface, offering a service to other pieces of software. A document or standard that describes how to build or use such a connection or interface is called an ''API specification''. A computer system that meets this standard is said to ''implement'' or ''expose'' an API. The term API may refer either to the specification or to the implementation. In contrast to a user interface, which connects a computer to a person, an application programming interface connects computers or pieces of software to each other. It is not intended to be used directly by a person (the end user) other than a computer programmer who is incorporating it into the software. An API is often made up of different parts which act as tools or services that are available to the programmer. A program or a programmer that uses one of these parts is said to ''call'' that ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Data Compression
In information theory, data compression, source coding, or bit-rate reduction is the process of encoding information using fewer bits than the original representation. Any particular compression is either lossy or lossless. Lossless compression reduces bits by identifying and eliminating statistical redundancy. No information is lost in lossless compression. Lossy compression reduces bits by removing unnecessary or less important information. Typically, a device that performs data compression is referred to as an encoder, and one that performs the reversal of the process (decompression) as a decoder. The process of reducing the size of a data file is often referred to as data compression. In the context of data transmission, it is called source coding; encoding done at the source of the data before it is stored or transmitted. Source coding should not be confused with channel coding, for error detection and correction or line coding, the means for mapping data onto a signal. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Binary Alignment Map
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them. Before indexing, BAM must be sorted by reference ID and then leftmost coordinate. BAM is in compressed BGZF format. The structure of BAM files include a header section and an alignment section: * Header—The sample name, sample length, and alignment method are all included in this section. The alignments section contains alignments that are linked to specific information in the header section. * Alignments—The read name, read sequence, read quality, alignment information, and custom tags are all included in this file. The chr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
File Format
A file format is a standard way that information is encoded for storage in a computer file. It specifies how bits are used to encode information in a digital storage medium. File formats may be either proprietary or free. Some file formats are designed for very particular types of data: PNG files, for example, store bitmapped images using lossless data compression. Other file formats, however, are designed for storage of several different types of data: the Ogg format can act as a container for different types of multimedia including any combination of audio and video, with or without text (such as subtitles), and metadata. A text file can contain any stream of characters, including possible control characters, and is encoded in one of various character encoding schemes. Some file formats, such as HTML, scalable vector graphics, and the source code of computer software are text files with defined syntaxes that allow them to be used for specific purposes. Specifications ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metagenome
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
