Biotechnology and Bioinformatics (1+1)

10.1.4 Databases

There are two types of databases i.e. Primary databases and Secondary databases.

Primary Database

Primary databases contain information and annotations of DNA and protein sequences, DNA and protein structure and DNA and Protein expresses profiles.

1. Genome Database

1. Sequence Database
2. Structural Database
1. Protein Database
   1. Structural Database
2. Complex Database
   1. Protein Nucleic acid Complex Database

Secondary Database

Those data that are derived from the analysis or treatment of primary data such as secondary structures, hydrophobicity plots, and domain are stored in secondary databases.

They also contain results of analysis of a primary resources including information as sequences patterns of methods, variants, mutation and evolutionary relationships.

1. Protein Database
   1. Sequence Database
2. Complex Database
   1. Protein Nucleic Acid Interaction Database

Primary sequence database for nucleic acid

GenBank

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. There are approximately 85,759,586,764 bases in 82,853,685 sequence records in the traditional GenBank divisions and 108,635,736,141 bases in 27,439,206 sequence records in the WGS division as of February 2008.

It maintains the following databases and tools:

1. Uterative Databases e.g. PUBMED, OMIMO

2. Entrey Databases e.g. Connoted Domain Databases, 3D Domains

3. Nueleotide Databases e.g. Expressed sequence Tags(EST)

4. Tools for Sequence analysis e.g. BLAST

5. Tools for 3-D structure display and similarity searching e.g. Cn3D

Databases consisting of data derived experimentally such as nucleotide sequences and three dimensional structures are known as primary databases.

EMBL

The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 20 European countries and Australia as associate member state.

In 1974, EMBL was created and it is a non-profit organisation funded by public research money from its member states.

Research at EMBL is conducted by approximately 85 independent groups covering the spectrum of molecular biology. The cornerstones of EMBL's mission are:

• to perform basic research in molecular biology and molecular medicine,
• to train scientists, students and visitors at all levels, to offer vital services to scientists in the member states,
• to develop new instruments and methods in the life sciences, and to actively engage in technology transfer.

Website: WWW.ebi.ac.UK

DDBJ

The DNA Data Bank of Japan is a DNA data bank. It is located at the National Institute of Genetics of Japan.

It shares its data with European Molecular Biology Laboratory at the European Bioinformatics Institute and with GenBank at the National Center for Biotechnology Information.

The DNA Data Bank of Japan (DDBJ, has made an effort to collect as much data as possible mainly from Japanese researchers. The increase rates of the data collected, annotated and released to the public in the past year are 43% for the number of entries and 52% for the number of bases.

The increase rates are accelerated even after the human genome was sequenced, because sequencing technology has been remarkably advanced and simplified, and research in life science has been shifted from the gene scale to the genome scale.

Search is done by FASTA and BLAST. Analysis is done by clustalW.