EMBL - Access the Database

The EMBL Nucleotide Sequence Database can be accessed a variety of ways. You can query the database using the SRS system or choose an access method from the following tables.

Mirror sites providing access to EMBL release and cumulative update files:
Denmark, Finland, USA, Japan, Australia.

Query the Databases

Link	Explanation
Genomes	Completed Genomes Webserver
SRS	Query all databases [EMBL-related libraries] [help]
Simple sequence retrieval	Sequence retrieval by accession number
EMBL Sequence Version Archive: browse or batch retrieval	Archive of all entries [help]
Browse data by geography	Geographical Origin of Sequenced Samples

FTP Server

Link	Explanation
/pub/databases/embl/	Sub-directories related to the EMBL database
/pub/databases/embl/genomes/	Finished genomes, chromosomes and contigs
/pub/databases/embl/release/	Complete latest full release of the EMBL Nucleotide Sequence Database
/pub/databases/embl/cds/	Nucleotide sequences of the CDS (coding sequence) features, as annotated in EMBL database (EMBLCDS dataset)
/pub/databases/embl/wgs/	Whole genome shotgun sequences
/pub/databases/embl/align/	Complete list of sequence alignment data
Old Format Alignments	List of old format alignments on FTP server (ds prefix)
/pub/software/	Freely available molecular biology software
/pub/databases/embl/patent/	Sequences from the patent literature
EST	EBI mirror of dbEST resources of the NCBI.
STS	EBI mirror of dbSTS resources of the NCBI.
ERA	European Read Archive (ERA).

Tools

Link	Explanation
BLAST2-WU Nucleotide	Washington University (WU) BLAST2 for nucleotide databases. (BLAST 2.0 with gaps)
BLAST2-NCBI Nucleotide	NCBI BLAST2 (BLASTALL) program for nucleotide databases.
FASTA Nucleotide	Sequence similarity searching against nucleotide databases using FASTA.
FASTA-Genome server	Completed Genomes FASTA server.
FASTA-WGS server	Whole genome shotgun (WGS) FASTA server.

For more similarity and homology tools check http://www.ebi.ac.uk/Tools/similarity.html

Mirror Sites

Location	URL
UK (EBI Server)	ftp://ftp.ebi.ac.uk/pub/databases/embl/release
France	ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release
Finland	ftp://ftp.funet.fi/pub/sci/molbio/embl_release/
USA	ftp://bio-mirror.net/biomirror/embl/release/
Japan	ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release/
China	ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/
Australia	ftp://biomirror.aarnet.edu.au/biomirror/embl/release