EMBL Nucleotide Sequence Data

The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Data Library, European Molecular Biology Laboratory, Postfach 10 22 09, D-6900 Heidelberg, F.R.G. 

The analysis was performed on a IBM PC/AT computer with IBI/Pustell Sequence Analyses Programs. Sequence data were obtained from GenBank Genetic Sequence Data Bank R.48.0, The EMBL Nucleotide Sequence Data Library and also from our own chloroplast gene library. 

Sequences of the genes/cDNAs can be retrieved from databases on the Internet at various web sites. For example, GeneBank (at the National Center for Biotechnology Information, NCBI) is at http //www.ncbi.nlm.nih.gov/ Web/Search/index.html. The EMBL Nucleotide Sequence database (through the European Bioinformatic Institute, EBI) can be found at http //www.ebi.ac.uk/queries/queries.html, whilst that of the DNA Data Bank of Japan is at http //www.ddbj.nig.ac.jp/. 

The SWISS-PROT and TrEMBL ID lines differ in the first two parts of the ID line. The first part is the entry name "ANP NOTCO" in the case of the SWISS-PROT example and "Q12757" in the TrEMBL example. The entry name used in all SP-TrEMBL entries is always the same as the accession number of the entry. The entry name used in REM-TrEMBL is the Protein ID tagged to the corresponding CDS in the EMBL Nucleotide Sequence Database. To the right of the entry name you will find either "preliminary" (in the TrEMBL entry) or STANDARD (in the SWISS-PROT entry). The data class used in TrEMBL is always PRELIMINARY. That means that the data are thoroughly checked by a computer,... 

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. 

GCRDb entry is not much more extensive than what is found in the EMBL nucleotide sequence entry from which it is derived. What makes this database useful are not the entries themselves, but the analyses (e.g., multiple alignments, classification into subfamilies) that have been made on the data and that are available from the GCRDb database. It is a good example of a specialized database adding value by offering an analytical view on data that a universal sequence database is unable to provide. 

The sequence data is compared to one or more of a proprietary (Microseq) or public (GenBank, http //www.ncbi.nlm.nih.gov EMBL Nucleotide Sequence Databank, http //www.ebi.ac.uk/embl/ DNA Data Bank of Japan (DDBJ), http //www.ddbj.nig.ac.jp/) database for identification. Frequently, only a portion of the gene, such as the internal transcribed spacer (ITS) regions, especially the ITSl region of SSU rDNAl 30>55.56,58,59 variable D2 region of the LSU rDNA,l >53... 

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 Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

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)... 

The European Bioinformatics Institute (EBI). This site is located at Hinxton Hall, Cambridge, UK. The home of the EMBL Nucleotide Sequence Database data management tools [including publicly accessible version of SRS—the Sequence Retrieval System (7)] protein family databases microarray tools etc. An extensive repository of resources for bioinformatics. 

EMBL Nucleotide Sequence DB at EBI DNA Data Bank of Japan (DDBJ) ... 

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. 

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. 

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... 

EMBL Data Library The main role of the European Molecular Biology Laboratory Data Library, currently known as EBI, is to maintain and distribute a database of nucleotide sequences. This work is a collaborative effort with GenBank and DNA Database of Japan (DDBJ) where each participating group collects a portion of the total reported sequence data. 

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. 

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. 

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