EMBL-GenBank

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. 

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. 

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)... 

Leffers, H., Stetter, K.O. and Garrett, R.A. (1993) EMBL/GenBank databases. Accession Number X72728. 

Kaine, B.P., Schurke, C. and Stetter, K..O. (1991) EMBL/GenBank databases. Accession Number M21087. 

Accession numbers starting with P-Q are from the Swiss-Prot databank, others from the EMBL/GenBank ( crystal structure reference). 

DR EMBL M19283 AAA51579.1 [EMBL / GenBank / DDBJ1 [CoDingSeouence]... 

EMBL/GenBank/DDBJ is an archive or repository database. In that respect, no attempt is made to reduce the size of the database by merging entries submitted by different groups and which correspond to the same... 

If it is necessary to upload sequence files, these can be compressed using either WinZip, or the UNIX gzip utility, which will significantly reduce the time taken to upload the data. Submitted files should each contain a single sequence in EMBL or FASTA format. It is preferable to use EMBL/Genbank format for uploaded sequences, because any genes annotated in the feature table will then be displayed by ACT. Should multiple sequences be present in an uploaded file, only the first will be used. 

Within the computer science community, regular expressions may be considered a standard [3]. The Open Group has an online standard on this topic (table 2.4). They are working to unify various approaches, including Unix and Perl 5 regular expressions. On the life sciences side, the controlled vocabularies provided by DDBJ/EMBL/GenBank and Swiss-Prot features are de facto standards. 

Although the DDBJ/EMBL/GenBank feature table allows numerous kinds of features to be included (see Chapter 3), the NCBI data model treats some features as more equal than others. Specifically, certain features directly model the central dogma of molecular biology and are most likely to be used in making coimections between records and in discovering new information by computation. These features are discussed next. 

DNA sequence records from the public databases (DDBJ/EMBL/GenBank) are essential components of computational analysis in molecular biology. The sequence records are also reagents for improved curated resources like LocusLink (see Chapter... 

CONTACT POINTS FOR SUBMISSION OF SEQUENCE DATA TO DDBJ/EMBL/GenBank... 

DDBJ/EMBL/GenBank Feature Table Documentation EMBL Release Notes... 

The UniProt Archive (UniParc) provides a stable, comprehensive, nonredundant sequence collection by storing the complete body of publicly available protein sequence data. Although most protein sequence data are derived from the translation of DDBJ/EMBL/GenBank sequences, primary protein sequence data are also submitted directly to UniProt or derived from the PDB entries. The Archive also captures protein sequence data from other sources such as Ensemble, International Protein Index (IPI), NCBI-RefSeq, FlyBase, and WormBase. Each protein sequence is assigned to a unique UniParc identifier (UPI ) and represented only once in the Archive. In UniParc, the... 

Protein Identification Resource National Biomedical Research Foundation Georgetown University Medical Center 3900 Reservoir Road, N.W., Washington, DC 20007 Contains nucleotide and amino acid sequences not as extensive in nucleotide sequences as EMBL-GenBank good program environment for quick and easy data retrieval... 

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