9 Genomic Techniques and How to Apply Them to Marine Questions
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(b) EMBL at the EBI
EMBL-Bank (Cochrane et al. 2008) was created in 1981 at the European Molecular
Biology Laboratory (EMBL) in Heidelberg, Germany. It moved in 1993 to the
European Bioinformatics Institute (EBI) outstation in Hinxton near Cambridge,
UK, to be closer to genome research institutes such as the Wellcome Trust Sanger
Institute. EMBL-Bank now forms part of the Protein and Nucleotide Database
Group (PANDA) at the EBI.
A sample entry in EMBL flat file format can be found in the regularly updated
DDBJ/EMBL/GenBank Feature Table file on the EMBL website.
Several other useful EMBL annotation examples can be found on the EMBL
website.
The EMBL nucleotide sequence database can be accessed in a number of ways
(see Table 9.8).
Table 9.8 The different ways to retrieve data at EMBL
Sequence retrieval at EMBL
Simple sequence retrieval
(embl fetch)
Sequence retrieval by accession number
SRS
Query all databases by term search, including
EMBL-Bank standard, EST, STS and GSS data
EMBL sequence version archive
Repository of all current and historical EMBL
entries
Browse data by geography
Geographical origin of sequenced samples
FTP server
Complete latest EMBL release, completed genomes,
contigs, WGS sequences, patent sequences, etc.
Genomes
Access to completed genomes
Genome reviews
Genome annotation of Archaea, Bacteria,
bacteriophages and selected Eukaryota
Ensembl genome browser
Annotation of large eukaryotic genomes
Integr8
Proteome analysis information
(c) GenBank at NCBI
The GenBank nucleotide sequence database (Benson et al. 2008) was created in
1982 at the Los Alamos National Laboratory (LANL) in the USA. It moved in
1993 to the National Institute of Biotechnology Information (NCBI) in Bethesda,
Maryland.
A sample entry in GenBank flat file format can be found in the regularly updated
DDBJ/EMBL/GenBank Feature Table file on the NCBI website.
Several useful annotation examples in GenBank flat-file format can be found on
the BankIt website.
The GenBank nucleotide sequence database can be accessed in a number of ways
(see Table 9.9).
349
(b) EMBL at the EBI
EMBL-Bank (Cochrane et al. 2008) was created in 1981 at the European Molecular
Biology Laboratory (EMBL) in Heidelberg, Germany. It moved in 1993 to the
European Bioinformatics Institute (EBI) outstation in Hinxton near Cambridge,
UK, to be closer to genome research institutes such as the Wellcome Trust Sanger
Institute. EMBL-Bank now forms part of the Protein and Nucleotide Database
Group (PANDA) at the EBI.
A sample entry in EMBL flat file format can be found in the regularly updated
DDBJ/EMBL/GenBank Feature Table file on the EMBL website.
Several other useful EMBL annotation examples can be found on the EMBL
website.
The EMBL nucleotide sequence database can be accessed in a number of ways
(see Table 9.8).
Table 9.8 The different ways to retrieve data at EMBL
Sequence retrieval at EMBL
Simple sequence retrieval
(embl fetch)
Sequence retrieval by accession number
SRS
Query all databases by term search, including
EMBL-Bank standard, EST, STS and GSS data
EMBL sequence version archive
Repository of all current and historical EMBL
entries
Browse data by geography
Geographical origin of sequenced samples
FTP server
Complete latest EMBL release, completed genomes,
contigs, WGS sequences, patent sequences, etc.
Genomes
Access to completed genomes
Genome reviews
Genome annotation of Archaea, Bacteria,
bacteriophages and selected Eukaryota
Ensembl genome browser
Annotation of large eukaryotic genomes
Integr8
Proteome analysis information
(c) GenBank at NCBI
The GenBank nucleotide sequence database (Benson et al. 2008) was created in
1982 at the Los Alamos National Laboratory (LANL) in the USA. It moved in
1993 to the National Institute of Biotechnology Information (NCBI) in Bethesda,
Maryland.
A sample entry in GenBank flat file format can be found in the regularly updated
DDBJ/EMBL/GenBank Feature Table file on the NCBI website.
Several useful annotation examples in GenBank flat-file format can be found on
the BankIt website.
The GenBank nucleotide sequence database can be accessed in a number of ways
(see Table 9.9).