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A database is a vast collection of data pertaining to
a specific topic, e.g., nucleotide sequence, protein
sequence, etc. in an electronic environment.
Databases are at the heart of bioinformatics. There
is a very large number of databases, which is
growing rapidly. The biological information can be
stored in different databases. Each database has its
own website with unique navigation tools. The
biological databases are, in general, publicly
accessible.
Types of databases: 3 types on the basis of source.
Primary databases:
Primary databases contain original biological data. They are
archives of raw sequence or structural data submitted by the
scientific community. It can also be called an archival database since
it archives the experimental results submitted by the scientists. The
primary database is populated with experimentally derived data like
genome sequence, macromolecular structure, etc.
The data are given accession numbers when they are entered into the
database. The same data can later be retrieved using the accession
number. Accession number identifies each data uniquely and it
never changes.
Examples –
Nucleotide sequence:
European Molecular Biology Laboratory (EMBL) database,
GenBank and
DDBJ
Protein Databases are: PDB, PIR, Metacyc, etc.
GenBank
GenBank is physically located in the USA and is
accessible through the NCBI portal over the intern.
The GenBank sequence database is open access,
annotated collection of all publicly
available nucleotide sequences and
their protein translations. This database is produced
and maintained by the National Center for
Biotechnology Information (NCBI) as part of
the International Nucleotide Sequence Database
Collaboration (INSDC). GenBank has become an
important database for research in biological fields
and has grown in recent years at an exponential
rate by doubling roughly every 18 months.
EMBL (European Molecular Biology
Laboratory)
EMBL (European Molecular Biology
Laboratory) is in UK. The European
Molecular Biology Laboratory (EMBL)
Nucleotide Sequence Database is a
comprehensive collection of primary
nucleotide sequences maintained at the
European Bioinformatics Institute (EBI).
Data are received from genome
sequencing centers, individual scientists
and patent offices.
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