GenBank nucleotide sequence database

PIR provides also some degree of crossreferencing to other biomolecu-lar databases by linking to the DDBJ/EMBL/GenBank nucleotide sequence databases, PDB, GDB, FlyBase, OMIM, SGD, and MGD. 

The next lines, the OS (Organism Species) and OC (Organism Classification), describe the species from which the protein has been derived. The OS line shows the scientific name of the organism and, if existing, the common English name. The OC lines give the taxonomic tree. SWISS-PROT, as well as the DDBJ/EMBL/GenBank nucleotide sequence databases, uses the NCBI taxonomy to standardize the taxonomies of the molecular sequence databases. 

The UniProt KB is an automatically and manually annotated protein database drawn from translation of DDBJ/EMBL-Bank/GenBank coding sequences and directly sequenced proteins. Each sequence receives a imique, stable identifier allowing unambiguous identification of any protein across datasets. The KB also provides cross-references to external data collections such as the underlying DNA sequence entries in the DDBJ/EMBL-Bank/GenBank nucleotide sequence databases, 2D PAGE and 3D protein structure databases, various protein domain... 

GenBank (NCBI, USA) EMBL Nucleotide Sequence Database (Europe) DDBJ (Japan) The three main nucleotide sequence databases, which are synchronised daiiy... 

Various verification steps have been introduced to ensure that SPTR is comprehensive and contains all relevant data sources. The main source of new protein sequences is the translations of CDS in the nucleotide sequence databases. The up-to-date inclusion of new protein sequence entries is ensured by the weekly translation of EMBL-NEW (the updates to the EMBL nucleotide sequence database). The three collaborating nucleotide sequence databases DDBJ, EMBL, and GenBank exchange their data on a daily basis. Therefore any protein coding sequence submitted to DDBJ/EMBL/GenBank will appear in SPTR within 2 weeks in the worst case and within less than 1 week in the average case. 

GenBank is the NIH genetic sequence database, and an annotated collection of all publicly available DNA sequences. It is part of the International Nucleotide Sequence Database Collaboration, which comprises the GenBank at NCBI, DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL). These three organizations exchange data on a daily basis. 

One of the central activities of the European Bioinformatics Institute (EBI) (Emmert et ah, 1994) is development and distribution of the EMBL nucleotide sequence database (Stoesser et ah, 2001). This is a collaborative project with GenBank (NCBI, USA) and DDBJ (DNA database of Japan) to ensure that all the new and updated database entries are shared between the groups on a daily basis. The search of sequence databases and an access to various application tools can be approached from the home page of EBI at http //www.ebi.ac.uk/ (Figure 3.3). 

The nucleotide sequences can be retrieved from one of the three IC (International Collaboration) nucleotide sequence repositories/databases GenBank, EMBL Nucleotide Sequence Database, and DNA Data Bank of Japan (DDBJ). The retrieval can be conducted via accession numbers or keywords. Keynet (http // www.ba.cnr.it/keynet.html) is a tree browsing database of keywords extracted from... 

EMBL—the European Molecular Biology Laboratory (Heidelberg) Nucleotide Sequence Database (also known as EMBL-Bank). The database is produced in an international collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ). The EMBL nucleotide sequence database is part of the Protein and Nucleotide Database Group (PANDA). 

DNA sequence The nucleotide sequence data are available from the EMBL, GenBank, and DDBJ Nucleotide Sequence Databases under accession number X52255 Half-life About 20 min (experimentally determined for human cystatin C in rat plasma. The similarity in distribution volume and renal clearance between human cystatin C and acknowledged markers of human glomerular filtration, i.e., iohexol and 51 Cr-EDTA, suggests that the substances are eliminated at the same rate in humans with a half-life of approximately 2 h in individuals with normal renal function)... 

International Nucleotide Sequence Database. URL http // www.ddbj.nig.ac.jp/. A joint compilation of heterogeneous sequence data into a redundant database. New and updated data shared daily by DNA Database of Japan (DDBJ). European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBD- Cambridge, U.K. URL http // www.ebi.ac.uk/Databases/. GenBank. NCBI. URL http // www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html. 

GenBank, EMBL, and DDBJ form the International Nucleotide Sequence Database Collaboration. The partnership databases are the richest source of publicly available annotated nucleotide sequences. The FT describes the features and syntax [28]. Although not all features involve patterns, many do. Examples include... 

Field/value-based flat files have been very commonly used in bioinformatics. Examples are the flat file libraries from GenBank, European Molecular Biology Laboratory Nucleotide Sequence Database (EMBL), DNA Data Bank of Japan, or Universal Protein Resource (UniProt). These file types are a very limited solution because they lack referencing, vocabulary control, and constraints. In addition, on the file level, there is no inherent locking mechanism that detects when a file is being used or modified. However, these file types are primarily used for reading purposes. 

Recently, the members of the International Nucleotide Sequence Database Collaboration (GenBank, EMBL, and DDBJ) introduced a better sequence identifier, one that combines an accession (which identifies a particular sequence record) with a version number (which tracks changes to the sequence itself). It is expected that this kind of Seq-id will become the preferred method of citing sequences. 

A full release of GenBank occins on a bimonthly schedule with incremental (and nonincremental) daily updates available by anonymous FTP. The International Nucleotide Sequence Database Collaboration also exchanges new and updated records daily. Therefore, all sequences present in GenBank are also present in DDBJ and EMBL, as described in the introduction to this chapter. The three databases rely on a common data format for information described in the feature table documentation (see below). This represents the lingua franca for nucleotide sequence database annotations. Together, the nucleotide sequence databases have developed defined submission procedures (see Chapter 4), a series of guidelines for the content and format of all records. 

The partners of the International Nucleotide Sequence Databases (INSD), namely GenBank, EMBL, and DDBJ, share their nucleic acid... 

The increasing numbers of stored protein and nucleic acid sequences, and the recognition that functionally related proteins often had similar sequences, catalyzed the development of statistical techniques for sequence comparison which underlie many of the core bioinformatic methods used in proteomics today. Nucleic acid sequences are stored in three primary sequence databases - GenBank, the EMBL nucleotide sequence database, and the DNA database of Japan (DDBJ) - which exchange data every day. These databases also contain protein sequences that have been translated from DNA sequences. A dedicated protein sequence database, SWISS-PROT, was founded in 1986 and contains highly curated data concerning over 70 000 proteins. A related database, TrEMBL, contains automatic translations of the nucleotide sequences in the EMBL database and is not manually curated. 

The nucleotide sequence data reported in this paper will appear in the EMBL, GenBank and DDBJ Nucleotide Sequence Databases under the accession number X79677. 

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