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Sequence Database
In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("Digital data, digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. The UniProt database is an example of a protein sequence database. As of 2013 it contained over 40 million sequences and is growing at an exponential rate. Historically, sequences were published in paper form, but as the number of sequences grew, this storage method became unsustainable. Search Searching in a sequence database involves looking for similarities between a genomic/protein sequence and a query string and, finding the sequence in the database that "best" matches the target sequence (based on criteria which vary depending on the search method). The number of matches/hits is used to formulate a score that determines the similarity between the sequence query and the sequences in the sequence database. The main goal is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA Format
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format allows for sequence names and comments to precede the sequences. It originated from the FASTA software package and has since become a near-universal standard in bioinformatics. The simplicity of FASTA format makes it easy to manipulate and parse sequences using text-processing tools and scripting languages. Overview A sequence begins with a greater-than character (">") followed by a description of the sequence (all in a single line). The lines immediately following the description line are the sequence representation, with one letter per amino acid or nucleic acid, and are typically no more than 80 characters in length. For example: >MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTV ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Information Resource
The Protein Information Resource (PIR), located at Georgetown University Medical Center, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies. It contains protein sequences databases History PIR was established in 1984 by the National Biomedical Research Foundation as a resource to assist researchers and customers in the identification and interpretation of protein sequence information. Prior to that, the foundation compiled the first comprehensive collection of macromolecular sequences in the Atlas of Protein Sequence and Structure, published from 1964 to 1974 under the editorship of Margaret Dayhoff. Dayhoff and her research group pioneered in the development of computer methods for the comparison of protein sequences, for the detection of distantly related sequences and duplications within sequences, and for the inference of evolutionary histories from alignments of protein sequences. Winona Barker and Robert Ledle ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SwissProt
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 Uni ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Third Party Annotation
Third or 3rd may refer to: Numbers * 3rd, the ordinal form of the cardinal number 3 * , a fraction of one third * 1⁄60 of a ''second'', i.e., the third in a series of fractional parts in a sexagesimal number system Places * 3rd Street (other) * Third Avenue (other) * Highway 3 Music Music theory *Interval number of three in a musical interval **Major third, a third spanning four semitones **Minor third, a third encompassing three half steps, or semitones **Neutral third, wider than a minor third but narrower than a major third **Augmented third, an interval of five semitones **Diminished third, produced by narrowing a minor third by a chromatic semitone *Third (chord), chord member a third above the root *Degree (music), three away from tonic **Mediant, third degree of the diatonic scale **Submediant, sixth degree of the diatonic scale – three steps below the tonic ** Chromatic mediant, chromatic relationship by thirds *Ladder of thirds, similar to the c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RefSeq
The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. RefSeq was introduced in 2000. This database is built by National Center for Biotechnology Information (NCBI), and, unlike GenBank, provides only a single record for each natural biological molecule (i.e. DNA, RNA or protein) for major organisms ranging from viruses to bacteria to eukaryotes. For each model organism, ''RefSeq'' aims to provide separate and linked records for the genomic DNA, the gene transcripts, and the proteins arising from those transcripts. ''RefSeq'' is limited to major organisms for which sufficient data are available (121,461 distinct "named" organisms as of July 2022), while GenBank includes sequences for any organism submitted (approximately 504,000 formally described species). RefSeq categories RefSeq collection comprises different data types, with different origins, so it is neces ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
National Institute Of Health
The National Institutes of Health (NIH) is the primary agency of the United States government responsible for biomedical and public health research. It was founded in 1887 and is part of the United States Department of Health and Human Services (HHS). Many NIH facilities are located in Bethesda, Maryland, and other nearby suburbs of the Washington metropolitan area, with other primary facilities in the Research Triangle Park in North Carolina and smaller satellite facilities located around the United States. The NIH conducts its scientific research through the NIH Intramural Research Program (IRP) and provides significant biomedical research funding to non-NIH research facilities through its Extramural Research Program. , the IRP had 1,200 principal investigators and more than 4,000 postdoctoral fellows in basic, translational, and clinical research, being the largest biomedical research institution in the world, while, as of 2003, the extramural arm provided 28% of biomed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...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] |
Similarity Matrix Of Proteins
Similarity Matrix of Proteins (SIMAP) is a database of protein similarities created using volunteer computing. It is freely accessible for scientific purposes. SIMAP uses the FASTA algorithm to precalculate protein similarity, while another application uses hidden Markov models to search for protein domains. SIMAP is a joint project of the Technical University of Munich, the Helmholtz Zentrum München, and the University of Vienna. Project The project usually got new work units at the beginning of each month. More recently, (2010), inclusion of environmental sequences into the database has required longer periods of activity, several months of continuous work for example. Typically, these updates occurred twice each year. In the fourth quarter of 2010, the project relocated to the University of Vienna due to the failing electrical infrastructure at the Technical University of Munich. Part of this exercise involved the creation of a project specific URL requiring existing voluntee ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wet Lab
A wet lab, or experimental lab, is a type of laboratory where it is necessary to handle various types of chemicals and potential "wet" hazards, so the room has to be carefully designed, constructed, and controlled to avoid spillage and contamination. A dry lab might have large experimental equipment but minimal chemicals, or instruments for analyzing data produced elsewhere. Overview A wet lab is a type of laboratory in which a wide range of experiments are performed, for example, characterizing of enzymes in biology, titration in chemistry, diffraction of light in physics, etc. - all of which may sometimes involve dealing with hazardous substances. Due to the nature of these experiments, the proper appropriate arrangement of safety equipment are of great importance. The researchers (the occupants) are required to know basic laboratory techniques including safety procedures and techniques related to the experiments that they perform. Laboratory design At the present, lab ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Database
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for museum collections etc.) Databases are important tools in assisting scientists to analyze and explain a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
