Biological Database

Nucleic acid database

 Biological Database:-

Biological databases are site that organize, store and

disseminate files that contain information consisting of
literature references, protein sequences and protein
structures .

 Why we need this biological database :-To existing

information to compare these data to find similarities
and differences .
 Biological database

Primary database Composite database Secondary database

Primary Database :-
The primary databases are those databases which is directly
come from laboratory and research field .

Primary database again classified into depend upon data present.

 Nucleic acid databases

Ex. 1) Gene bank
2) EMBL
3) DDBJ
 Protein sequence database
Ex. 1) PIR
2) MIPS
3) SWISS-PROT
4) TrEMBL
5) NRL- 3D
 Nucleic acid sequence database

Nucleic acid sequence database are collection

of entries . Each entry has the form a text file . Text
file contain text that Can be read by human being
as well as computer . text file contain data and
annotations for a single contiguous sequence.
Many entries are assembled from several
published papers reporting overlapping fragments
of a complete sequence. Each entry is divided into
fields. Fields are used to create indices for
relational databases. Each field is essentially a
table and the field values are indices. Unique
accession numbers are allotted.
 First nucleic acid sequence of yeast t-RNA
with 77 bases was announced around 1964
.there are three premier institutes in the world
,which constitute the International Nucleotide
sequence Database Collaboration These are
 NCBI
 EMBL
 DDBJ
Data are stored and exchanged daily. The
database contain not only sequences but
also extensive annotations.
 Gene Bank :
Gene bank stand form NCBI (national center for
biotechnology information )incorporates sequences from
publicly available sources, primarily form direct author
submissions and large-scale sequencing projects. It is a
generic sequence database. information can be retrieved
form Gene Bank using the Entrez integrated retrieval
system. Gene bank may be searched with user query
sequences by means of the NCBI Web interface to the
BLAST suite of programs.
The man purpose of the Gene Bank database is to
provide and encourage the scientific community to access
the most up to date and comprehensive DNA sequence
information.
 EMBL : (European Molecular Biology Laboratory )
EMBL conation sequences from direct author
submissions and genome sequencing groups and from
the scientific literature and patent applications. The
database is produced in collaboration with DDBJ and
Gene Bank ;the participating groups each collect a
portion of total sequence data reported worldwide, and
new updated entries are then exchanged between the
groups .
• DDBJ : (DNA Databank Japan )
DDBJ database is produced, maintained and distributed
at the National Institute of Genetics; sequence may be
submitted to it from all corners of the world by means of
a web-based data submission tool. The web is also used
to provide standard search such as FASTA and BLAST.