EMBL nucleotide sequence

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

Swiss-Prot, TrEMBL Annotated non-redundant protein sequence database, TrEMBL is a computer-annotated supplement to Swiss-Prot. TrEMBL contains the translations of all coding sequences present in the EMBL Nucleotide Sequence Database which are no yet integrated into Swiss-Prot... 

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 DR lines link SWISS-PROT to other biomolecular databases. SWISS-PROT is currently linked to 29 different databases. The preceding example shows links to 19 different entries in 6 different databases. The cross references allow users to navigate to linked databases to retrieve part or all of the related information. The format of a DR line, except for cross references to PROSITE (Hofmann et al., 1999), Pfam (Bateman et al., 1999), and the EMBL nucleotide sequence databases (Stoesser et al., 1999), is the following ... 

The specific format for cross references to the EMBL nucleotide sequence database is ... 

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... 

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 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. 

EMBL Nucleotide Sequence Database EMGlib Entrez EPD... 

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). 

UniProtKB/TrEMBL a computer-annotated supplement of Swiss-Prot that contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot. 

Other useful addresses, especially in the context of research on allergens in the fields of proteomics and genomics, are the databases on sequences of nucleotides corresponding to particular proteins or epitopes, e.g., The EMBL Nucleotide Sequence Database—http //www.ebi.ac.uk/embl/Access/, or the Protein and Nucleotide Database Group (PANDA)—http //www.ebi.ac.uk/panda/ or the database Ensembl— http //www.ensembl.org/index.html, http //www.ebi.ac.uk/ensembl/. 

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 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. 

Stoesser G., Tuli M., Lopez R., Sterk P. (1999) The EMBL Nucleotide Sequence Dabase. Nucleic Acids Res., 27 1, 18-24. 

Kanz, C., R Aldebert, N. Althorpe, W. Baker, A. Baldwin, K. Bates, R Browne, et al. 2005. The EMBL nucleotide sequence database. Nucleic Acids Res 33, Database Issue D29-33. 

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

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. 

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. 

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