In the field of bioinformatics , a sequence database is a type of biological database that is composed of a large collection of computerized (" 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.
22-495: PROSITE is a protein database . It consists of entries describing the protein families , domains and functional sites as well as amino acid patterns and profiles in them. These are manually curated by a team of the Swiss Institute of Bioinformatics and tightly integrated into Swiss-Prot protein annotation. PROSITE was created in 1988 by Amos Bairoch , who directed the group for more than 20 years. Since July 2018,
44-638: A deeper comparative analysis of proteins than ever before. This led to many developments such as, probabilistic models of amino acid substitutions, sequence aligning and phylogenetic trees of evolutionary relationships of proteins. Entire sequencing process became fully automated. The first nucleotide sequence database was created. Previously known as the European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Data Library (now known as European Nucleotide archive). Human Genome Project began in 1988. The project's goal
66-675: A limited number of reference sequences. A paper released in the Journal of Clinical Microbiology evaluated the 16S rRNA gene sequencing results analyzed with GenBank in conjunction with other freely available, quality-controlled, web-based public databases, such as the EzTaxon -e and the BIBI databases. The results showed that analyses performed using GenBank combined with EzTaxon -e (kappa = 0.79) were more discriminative than using GenBank (kappa = 0.66) or other databases alone. GenBank, being
88-853: A public database, may contain sequences wrongly assigned to a particular species, because the initial identification of the organism was wrong. A recent article published in Genome showed that 75% of mitochondrial Cytochrome c oxidase subunit I sequences were wrongly assigned to the fish Nemipterus mesoprion resulting from continued usage of sequences of initially misidentified individuals. The authors provide recommendations how to avoid further distribution of publicly available sequences with incorrect scientific names. Numerous published manuscripts have identified erroneous sequences on GenBank. These are not only incorrect species assignments (which can have different causes) but also include chimeras and accession records with sequencing errors. A recent manuscript on
110-441: A result, the sequences themselves, and especially the biological annotations attached to these sequences, may vary in quality. There is much redundancy, as multiple labs may submit numerous sequences that are identical, or nearly identical, to others in the databases. Many annotations of the sequences are based not on laboratory experiments, but on the results of sequence similarity searches for previously annotated sequences. Once
132-425: 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
154-414: A sequence has been annotated based on similarity to others, and itself deposited in the database, it can also become the basis for future annotations. This can lead to a transitive annotation problem because there may be several such annotation transfers by sequence similarity between a particular database record and actual wet lab experimental information. Therefore, care must be taken when interpreting
176-775: Is an open access , annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part of the National Institutes of Health in the United States ) as part of the International Nucleotide Sequence Database Collaboration (INSDC). GenBank and its collaborators will receive sequences produced in laboratories throughout
198-454: Is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers. Only original sequences can be submitted to GenBank. Direct submissions are made to GenBank using BankIt, which is a Web-based form, or the stand-alone submission program, Sequin. Upon receipt of a sequence submission, the GenBank staff examines the originality of
220-743: Is part of the ExPASy proteomics analysis servers. The database ProRule builds on the domain descriptions of PROSITE. It provides additional information about functionally or structurally critical amino acids. The rules contain information about biologically meaningful residues, like active sites, substrate - or co-factor -binding sites, posttranslational modification sites or disulfide bonds, to help function determination. These can automatically generate annotation based on PROSITE motifs. As of 26 February 2022, release 2022_01 has 1,902 documentation entries, 1,311 patterns, 1,336 profiles, and 1,352 ProRules. Sequence database Searching in
242-457: Is to have a good balance between the two criteria. The need for sequence databases originated in 1950 when Fredrick Sanger reported the primary structure of insulin. He won his second Nobel Prize for creating methods for sequencing nucleic acids, and his comparative approach is what sparked other protein biochemists to begin collecting amino acid sequences. Thus marking the beginning of molecular databases. In 1965 Margaret Dayhoff and her team at
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#1732801893562264-518: The GenBank project transitioned to the newly created National Center for Biotechnology Information (NCBI) . The GenBank release notes for release 250.0 (June 2022) state that "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months". As of 15 June 2022, GenBank release 250.0 has over 239 million loci , 1,39 trillion nucleotide bases, from 239 million reported sequences. The GenBank database includes additional data sets that are constructed mechanically from
286-716: The National Biomedical Research Foundation (NBRF) published "The Atlas of Protein Sequence and Structure". They put all know protein sequences in the Atlas , even unpublished material. This can be seen as the first attempt to create a molecular database. They made use of the newly computerized (1964) Medical Literature Analysis and Retrieval System (MEDLARS) at the National Institutes of Health (NIH). The team used computers to store
308-702: The Theoretical Biology and Biophysics Group at Los Alamos National Laboratory (LANL) and others established the Los Alamos Sequence Database in 1979, which culminated in 1982 with the creation of the public GenBank. Funding was provided by the National Institutes of Health , the National Science Foundation , the Department of Energy , and the Department of Defense . LANL collaborated on GenBank with
330-480: The annotation data from sequence databases. Most of the current database search algorithms rank alignment by a score, which is usually a particular scoring system. The solution towards solving this issue is found by making a variety of scoring systems available to suit to the specific problem. When using a searching algorithm we often produce an ordered list which can often carry a lack of biological significance. GenBank The GenBank sequence database
352-561: The data and assigns an accession number to the sequence and performs quality assurance checks. The submissions are then released to the public database, where the entries are retrievable by Entrez or downloadable by FTP . Bulk submissions of Expressed Sequence Tag (EST), Sequence-tagged site (STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are most often submitted by large-scale sequencing centers. The GenBank direct submissions group also processes complete microbial genome sequences. Walter Goad of
374-621: The data but had to manually type and proofread each sequence, which had a high cost in time and money. In 1966 the team released the second edition of the Atlas, double the size of the first. It contained about 1000 sequences, and this time was coined as an information explosion. The National Biomedical Research Foundation (NBRF) was on the cutting edge of utilizing computers for medicine and biology at this time. Dayhoff and her team made use of their facilities for determining amino acid sequences of protein molecules in mainframe computers. The number of discovered sequences continued to grow allowing for
396-516: The director of PROSITE and Swiss-Prot is Alan Bridge. PROSITE's uses include identifying possible functions of newly discovered proteins and analysis of known proteins for previously undetermined activity. Properties from well-studied genes can be propagated to biologically related organisms, and for different or poorly known genes biochemical functions can be predicted from similarities. PROSITE offers tools for protein sequence analysis and motif detection (see sequence motif , PROSITE patterns ). It
418-588: The firm Bolt, Beranek, and Newman , and by the end of 1983 more than 2,000 sequences were stored in it. In the mid-1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL. As one of the earliest bioinformatics community projects on the Internet, the GenBank project started BIOSCI /Bionet news groups for promoting open access communications among bioscientists. During 1989 to 1992,
440-482: The main sequence data collection, and therefore are excluded from this count. Public databases which may be searched using the National Center for Biotechnology Information Basic Local Alignment Search Tool (NCBI BLAST), lack peer-reviewed sequences of type strains and sequences of non-type strains. On the other hand, while commercial databases potentially contain high-quality filtered sequence data, there are
462-498: The world from more than 500,000 formally described species . The database started in 1982 by Walter Goad and Los Alamos National Laboratory . GenBank has become an important database for research in biological fields and has grown in recent years at an exponential rate by doubling roughly every 18 months. Release 250.0, published in June 2022, contained over 17 trillion nucleotide bases in more than 2,45 billion sequences. GenBank
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#1732801893562484-431: Was sequence and map all the genes in a human which required the capability to create and utilize a large sequence database. We now have many sequence databases, tools for using them and easy access to them. One of the largest being GenBank which contains over 2 billion sequences. Records in sequence databases are deposited from a wide range of sources, from individual researchers to large genome sequencing centers. As
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