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BED (file Format)
The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented in the form of columns separated by spaces or tabs. This format was developed during the Human Genome Project and then adopted by other sequencing projects. As a result of this increasingly wide use, this format had already become a ''de facto'' standard in bioinformatics before a formal specification was written. One of the advantages of this format is the manipulation of coordinates instead of nucleotide sequences, which optimizes the power and computation time when comparing all or part of genomes. In addition, its simplicity makes it easy to manipulate and read (or parsing) coordinates or annotations using word processing and scripting languages such as Python, Ruby or Perl or more specialized tools such as BEDTools. History The end of the 20th century saw the emergence of the first projects to sequence complete ge ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Text File
A text file (sometimes spelled textfile; an old alternative name is flatfile) is a kind of computer file that is structured as a sequence of lines of electronic text. A text file exists stored as data within a computer file system. In operating systems such as CP/M and MS-DOS, where the operating system does not keep track of the file size in bytes, the end of a text file is denoted by placing one or more special characters, known as an end-of-file marker, as padding after the last line in a text file. On modern operating systems such as Microsoft Windows and Unix-like systems, text files do not contain any special EOF character, because file systems on those operating systems keep track of the file size in bytes. Most text files need to have end-of-line delimiters, which are done in a few different ways depending on operating system. Some operating systems with record-orientated file systems may not use new line delimiters and will primarily store text files with lines separat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, DNA Genographic Projects and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. Comparing healthy and mutated DNA sequences can diagnose different diseases including various cancers, characterize antibody repertoire, and can be used to guide patient treatment. Having a quick way to sequence DNA allows for faster and more individualized medical care to be administered, and for more organisms to be identified and cataloged. The rapid speed of sequencing attained with modern D ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tab-separated Values
A tab-separated values (TSV) file is a simple text format for storing data in a tabular structure, e.g., a database table or spreadsheet data, and a way of exchanging information between databases. Each record in the table is one line of the text file. Each field value of a record is separated from the next by a tab character. The TSV format is thus a variation of the comma-separated values format. TSV is a simple file format that is widely supported, so it is often used in data exchange to move tabular data between different computer programs that support the format. For example, a TSV file might be used to transfer information from a database program to a spreadsheet. The IANA standard for TSV achieves simplicity by simply disallowing tabs within fields. Example The head of the Iris flower data set can be stored as a TSV using the following plain text (note that the HTML rendering may convert tabs to spaces): Sepal length Sepal width Petal length Petal width&Tab ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Space (punctuation)
In writing, a space () is a blank area that separates words, sentences, syllables (in syllabification) and other written or printed glyphs (characters). Conventions for spacing vary among languages, and in some languages the spacing rules are complex. Inter-word spaces ease the reader's task of identifying words, and avoid outright ambiguities such as "now here" vs. "nowhere". They also provide convenient guides for where a human or program may start new lines. Typesetting can use spaces of varying widths, just as it can use graphic characters of varying widths. Unlike graphic characters, typeset spaces are commonly stretched in order to align text. The typewriter, on the other hand, typically has only one width for all characters, including spaces. Following widespread acceptance of the typewriter, some typewriter conventions influenced typography and the design of printed works. Computer representation of text facilitates getting around mechanical and physical limitations su ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scaffolding (bioinformatics)
Scaffolding is a technique used in bioinformatics. It is defined as follows: Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically contiguous sequences corresponding to read overlaps. When creating a draft genome, individual reads of DNA are second assembled into contigs, which, by the nature of their assembly, have gaps between them. The next step is to then bridge the gaps between these contigs to create a scaffold. This can be done using either optical mapping or mate-pair sequencing. Assembly software The sequencing of the ''Haemophilus influenzae'' genome marked the advent of scaffolding. That project generated a total of 140 contigs, which were oriented and linked using paired end reads. The success of this strategy prompted the creation of the software, Grouper, which was included in genome assemblers. Until 2001, this was the only scaffolding soft ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chromosome
A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are the histones. These proteins, aided by chaperone proteins, bind to and condense the DNA molecule to maintain its integrity. These chromosomes display a complex three-dimensional structure, which plays a significant role in transcriptional regulation. Chromosomes are normally visible under a light microscope only during the metaphase of cell division (where all chromosomes are aligned in the center of the cell in their condensed form). Before this happens, each chromosome is duplicated ( S phase), and both copies are joined by a centromere, resulting either in an X-shaped structure (pictured above), if the centromere is located equatorially, or a two-arm structure, if the centromere is located distally. The joined copies are now called si ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Global Alliance For Genomics And Health
The Global Alliance for Genomics and Health (GA4GH) is an international consortium that is developing standards for responsibly collecting, storing, analyzing, and sharing genomic data in order to enable an "internet of genomics". GA4GH was founded in 2013. GA4GH is founded on the '' Framework for the Responsible Sharing of Genomic and Health-related Data,'' which is based on the human right to benefit from scientific advances. Organization GA4GH maintained by four Host Institutions (Wellcome Sanger Institute, Broad Institute, Ontario Institute for Cancer Research and the European Bioinformatics Institute). Ewan Birney is the current GA4GH chair and Peter Goodhand is the Chief Executive Officer. Heidi Rehm and Kathryn North are the current Vice Chairs. Organizational members of the alliance include: Funding GA4GH is supported by a "Funder's Forum" composed of organizations whose funding commitments exceed USD $200,000 annually, for at least three years. Forum members inclu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UCSC Genome Browser
The UCSC Genome Browser is an online and downloadable genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major Model organism, model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found on the UCSC Genome Bioinformatics website. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resou ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genome Browser
In bioinformatics, a genome browser is a graphical interface for display of information from a biological database for genomic data. Genome browsers enable researchers to visualize and browse entire genomes with annotated data including gene prediction and structure, proteins, expression, regulation, variation, comparative analysis, etc. Annotated data is usually from multiple diverse sources. They differ from ordinary biological databases in that they display data in a graphical format, with genome coordinates on one axis with annotations or space-filling graphics to show analyses of the genes, such as the frequency of the genes, their expression profiles, etc. A large number of genome browsers are available, many of them free and with database accessible online. Among the best known are the UCSC Genome Browser, Ensembl Genome Browser and NCBI The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Sequenced Animal Genomes
This list of sequenced animal genomes contains animal species for which complete genome sequences have been assembled, annotated and published. Substantially complete draft genomes are included, but not partial genome sequences or organelle-only sequences. Porifera * ''Amphimedon queenslandica'', a sponge (2009) * '' Stylissa carteri'' (2016) * ''Ephydatia muelleri'' (2020) * ''Xestospongia testudinaria'' (2016) Ctenophora * ''Mnemiopsis leidyi'' (Ctenophora), (order Lobata) (2012/2013) * '' Hormiphora californensis'' (Ctenophora) (2021 ) * ''Pleurobrachia bachei'' (Ctenophora) (2014) Placozoa * ''Trichoplax adhaerens'', a Placozoan (2008) * ''Hoilungia hongkongensis'', nov. gen H13 Placozoan (2018) Cnidaria * ''Hydra vulgaris'', (previously ''Hydra magnipapillata''), a model hydrozoan (2010) * ''Nematostella vectensis'', a model anemone ( starlet sea anemone) (2007) * ''Aiptasia pallida'', a sea anemone (2015) * ''Acropora digitifera'', a coral (2011) * Renilla muelleri, an o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
General Feature Format
In bioinformatics, the general feature format (gene-finding format, generic feature format, GFF) is a file format used for describing genes and other features of DNA, RNA and protein sequences. GFF Versions The following versions of GFF exist: General Feature Format Version 2 generally deprecated * a derivative used by Ensembl Generic Feature Format Version 3*Genome Variation Format with additional pragmas and attributes for sequence_alteration features GFF2/GTF had a number of deficiencies, notably that it can only represent two-level feature hierarchies and thus cannot handle the three-level hierarchy of gene → transcript → exon. GFF3 addresses this and other deficiencies. For example, it supports arbitrarily many hierarchical levels, and gives specific meanings to certain tags in the attributes field. The GTF is identical to GFF, version 2. GFF general structure All GFF formats (GFF2, GFF3 and GTF) are tab delimited with 9 fields per line. They all share the same stru ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acids Research
''Nucleic Acids Research'' is an open-access peer-reviewed scientific journal published since 1974 by the Oxford University Press. The journal covers research on nucleic acids, such as DNA and RNA, and related work. According to the ''Journal Citation Reports'', the journal's 2021 impact factor is 19.160. The journal publishes two yearly special issues, the first issue of each year is dedicated to biological databases, published in January since 1993, and the other is devoted to papers describing web-based software resources of value to the biological community (web server A web server is computer software and underlying hardware that accepts requests via HTTP (the network protocol created to distribute web content) or its secure variant HTTPS. A user agent, commonly a web browser or web crawler, initiate ...s), published in July since 2003. References External links * * Archives , https://www.ncbi.nlm.nih.gov/pmc/journals/4/ Biochemistry journals Open access j ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
