Stockholm Bioinformatics Center, SBC
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Lecture 18 Jan 2001 Per Kraulis

Databases in bioinformatics

4. Nucleotide sequence databases

Primary nucleotide sequence databases

The databases EMBL, GenBank, and DDBJ are the three primary nucleotide sequence databases: They include sequences submitted directly by scientists and genome sequencing group, and sequences taken from literature and patents. There is comparatively little error checking and there is a fair amount of redundancy.

The entries in the EMBL, GenBank and DDBJ databases are synchronized on a daily basis, and the accession numbers are managed in a consistent manner between these three centers.

The nucleotide databases have reached such large sizes that they are available in subdivisions that allow searches or downloads that are more limited, and hence less time-consuming. For example, GenBank has currently 17 divisions.

There are no legal restrictions on the use of the data in these databases. However, there are patented sequences in the databases.


The EMBL (European Molecular Biology Laboratory) nucleotide sequence database is maintained by the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK. As of 16 Jan 2001, it contained 10,378,022 records with a total of 11,302,156,937 bases; see the EMBL DB statistics page.

It can be accessed and searched through the SRS system at EBI, or one can download the entire database as flat files. An example of what an entry looks like is given for the human raf oncogene protein, ID: HSRAFR.


The GenBank nucleotide database is maintained by the National Center for Biotechnology Information (NCBI), which is part of the National Institute of Health (NIH), a federal agency of the US government.

It can be accessed and searched through the Entrez system at NCBI, or one can download the entire database as flat files. An example of what an entry looks like is given for the human raf oncogene protein, Locus: HSRAFR.


The DNA Data Bank of Japan began as a collaboration with EMBL and GenBank. It is run by the National Institute of Genetics. One can search for entries by accession number, FASTA/BLAST, keywords and regular expressions.

Other nucleotide sequence databases

The following databases contain subsets of the EMBL/GenBank databases. Some also contain more information or links than the primary ones, or have a different organization of the data to better suit some specific purpose. However, the nucleotide sequences themselves should always be available in the EMBL/GenBank databases. In this sense, the databases below are secondary databases.


The UniGene system attempts to process the GenBank sequence data into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.


The Saccharomyces Genome Database (SGD) is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.

EBI Genomes

This web site provides access and statistics for the completed genomes, and information about ongoing projects.

Genome Biology

The Genome Biology site at NCBI contains information about the available complete genomes.


Ensembl is a joint project between EMBL-EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation of eukaryotic genomes.

Copyright © 2001 Per Kraulis $Date: 2001/01/19 11:50:19 $