EMBL Nucleotide Sequence Database Release 56

The EMBL Nucleotide Sequence Database was frozen to create Release 56 on 16-Sep-1998. The release contains 2,689,618 sequence entries comprising 1,904,091,473 nucleotides. This represents an increase of about 15,5 % over Release 55.

EST & GSS Database Files

In order to keep the size of the data files within reasonable limits for handling purposes, the EST division has been split into several files. (EST1.DAT - EST19.DAT), while the GSS division has been split into 4 files (GSS1.DAT - GSS4.DAT).

Database Growth Graph:

Issues to note:

During the collaborative meeting in May 1998 at the EBI the International Nucleotide Sequence Database Collaboration DDBJ/EMBL/GenBank came to the following decisions:

1. Long sequences - 350 kilobase limit relaxed

The current 350kb limit for the maximum sequence length for a a single database record will be relaxed. It was decided that the size limit for an EMBL/DDBJ/GenBank entry will remain 350 kb, unless

• a single gene exceeds 350 kb, in which case the creation of an entry containing a sequence longer than 350 is legal.
• unfinished HTG data (i.e. high-throughput sequences) can exceed the 350 kb limit,  once finished these are split up into segments <350 kb.

2. Online Journals in reference section

Also at the 1998 May Collaborative Meeting the need to represent references which are published only online has been discussed. Until final specifications for such references are available from library organisations, EMBL will present online references like this:

RA        Miller, A.
RT        Cloning and expression of a phospholipase gene
RL        Online Publication
RC        Online-Journal-name; Article Identifier; URL

3.  New /country Feature Qualifier

A new source related qualifier '/country' will be implemented in Feature Table Definition document 2.1 (December 1998) to specify the origin of DNA samples used for epidemiological or population studies.

Qualifier:      /country=" "
Definition:     Country of origin for DNA sample, intended
                for epidemiological or population studies.
Value format:   "any country from annex 7.5.7 of the Feature
                Table documentation"
Example:        "Canada"
Comment:        /country should be a single token taken from
                the controlled list of annex 7.5.7 of the
                feature table documentation. /country can
                also have the following format:
                country:sub_region,
                such as: /country="Canada:Vancouver".

4. New  nucleotide and protein sequence identifiers

Both nucleotide and protein identifiers will consist of a stable part which will not change, and a version part which will be incremented whenever the underlying nucleotide sequence or protein translation changes. The new form of identifiers will allow easier tracking of changes to nucleotide and protein identifiers by external  databases  compared to the current identifiers.

'Accession.Version' (eg, Z86131.1),

where the accession number part will be stable, but the version part will  be  incremented  when the sequence changes. A new linetype 'SV'  (Sequence Version) will be introduced to represent this information.
Example:

ID   DBSELBGEN  standard; DNA; PRO; 2196 BP.
AC   X99911;
SV   X99911.3

Protein Sequence Identifier

/protein_id="CAA12345.6"

The version number will change only when the protein sequence coded by the CDS  changes, while the stable part will remain unchanged. This qualifier will be valid only on CDS features which translate into a valid protein.
During a transition phase both the old and new forms of identifiers will be provided, e.g.:

FT   CDS             1124. .1939
FT                   /db_xref="PID:g45266"
FT                   /protein_id="CAA12345.6"
FT                   /db_xref="SWISS-PROT:P29808"
FT                   /gene="aacC3"
FT                   /product="aminoglycoside-(3)-N-acetyl-transferase isoenzyme
FT                   III"

Subject to synchronization amongst the international databases we plan to introduce the new form of nucleotide and protein identifiers early 1999.

Information by: EBI´s EMBL team

Resources and further information

• European Bioinformatics Institute (EMBL-EBI)
  http://www.ebi.ac.uk/
• EMBL Nucleotide Sequence Database homepages
  http://www.ebi.ac.uk/ebi_docs/embl_db/ebi/topembl.html
• Latest EMBL Nucleotide Sequence Database release
  ftp://ftp.ebi.ac.uk/pub/databases/embl/release/

Direct questions or comments to Bioinformer Editor. This page last modified Friday, 16 July, 1999.
ISSN 1462-1363. More information about the BioInformer.

(c) 1997-1999 EMBL-EBI. All Rights Reserved.