EMBL database

EMBL (http //www.ebi.ac.uk/embl), database of the European Bioinformatics Institute, a part of the European Molecular Biology Laboratory. 

European dynamic filter, 11 384 European Inventory of Existing Chemical Substances (EINECS), 26 901 European Molecular Biology Laboratory (EMBL) database, 12 512 European patent, 18 198 European Patent Classification (ECLA) scheme, 18 209, 230 European Patent Convention (EPC), 18 189, 191... 

The entries from the composite divisions of the EMBL database (HTG, STS, EST, and UNC) are now added to their relative taxonomic TrEMBLnew divisions. Then all hies are searched for entries that have recently been added to SWISS-PROT or TrEMBL and are thus missing a /dbxref = SWISS-PROT or a /dbxref = SPTREMBL qualifier in EMBL. These entries are removed. The entries put in the hies patent.dat, immuno.dat, smalls.dat, synthetic.dat and pseudo.dat are now already at the end of their production line. They are new entries in REM-TrEMBL (REMaining TrEMBL), which contains the entries (about 44,000 in release 10) that will not be included in SWISS-PROT. This section is organized in hve subsections ... 

Abbreviations S., Streptomyces Streptoallo., Streptoalloteichus M., Micromonospora B., Bacillus A, authors DS, direct submission to EMBL database p, partially sequenced r, resistance gene(s) outside biosynthetic clusters sp., species ssp., subspecies. 

The EMBL database is maintained by the Hinxton Outstation (Great Britain) of the European Mole-... 

Notably, the model generated contains one factor, E2F that is known to be involved in cell cycle regulation of genes [67]. The model appears to be very selective and only one match per 12 million base pairs of the mammalian sections of the EMBL database was found. Almost all matches (total of 59) are known Histone HI genes, except in the human section where the majority of matches (25) are within anonymous sequences. However, given the extraordinary specificity throughout the mammalian sections, it seems safe to assume that most of the unknown matches within the human database section actually identified new so far unannotated genes, that are subject to... 

The EMBL database is a model nucleotide database to consider. Each entry in the database is given a unique ID and information about the entry is presented in a semi-structured way. The actual nucleotide sequence is presented at the end of the entry. 

Figure 1.7 shows a subset of the rules for describing in entry in the EMBL database. The Wrt command is the instruction to write a string into a token table. 

The meta definition which describes the structure of the resource is also written using ICARUS. For the EMBL database this meta definition consists of the definition of several objects. 

Subset of rules describing an entry in the EMBL database. 

The EMBL library object, (Figure 1.8), defines the EMBL library as being part of the sequence library group, with the format being described in the EMBL FORMAT object (Figure 1.9) and the files which make up the EMBL database being all those files with the extension dat in the EMBL flat file directory. 

The EMBL FORMAT object contains a list of fields which make up the database. In our example EMBL database the library has 5 fields. 

The field information is related to a particular token table via the index-Token attribute in the Field object. Hence, when a particular piece of information from the description field of the EMBL databank is requested, SRS looks in the description field meta definition for the EMBL database... 

In this example, the sequences to be compared will be selected from the EMBL database, by entering their accession numbers in the relevant boxes. Sequences... 

Fig. 8. Comparison of Streptococcus pneumoniae sequences from EMBL database viewed in ACT.

EMBL Database Repository of all publicly available annotated nucleotide and protein sequences http //wrww.ebi.ac.uk/embl.html... 

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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