The document discusses several key nucleic acid and protein databases. It describes the Nucleic Acid Database, which provides 3D structure information about nucleic acids. It also discusses NCBI, a collection of biomedical databases including GenBank that are freely accessible online. Other databases mentioned include EMBL, DDBJ, PDB, Swiss-Prot, and UniProt, each of which archives and provides access to nucleotide or protein sequence data.

1. Madhubala.S
Assistant Professor
Department of Biotechnology
Sri Adi Chunchanagiri Women’s
College, Cumbum.

2. Nucleic acid database
 The nucleic acid database is a web portal providing access to
information about 3D nucleic acid structure and their
complex
 It was found in 1991 and distribute structural information
about nucleic acids
 The Nucleic acid databanks was established the focus was on
DNA structural biology
 Nucleic acid databanks has developed generalized software
for processing, archiving, querying and distributing
structural data for nucleic acid

4. NCBI ( national center for
biotechnological informations)
 NCBI is a part of United States National Library Of Medicine
(NLM) a branch of national institute of Health (NIH).
 It was found in 1988 at Bethesda, Maryland.
 NCBI has a series of data relevant to Biotechnology and
biomedicine and is an important bioinformatics tool.
 all the recorded databases can be access through Enterz.
 NCBI is a collection of freely accessible, downloadable, on-line
version of selected biomedical books
 NCBI along with EBI & CIB together form international sequence
database
 Major collaborative databases includes Gene Bank, EMBL, DDBJ
 Major NCBI databases includes Pubmed for bibliographic
database, NCBI epigenomics,

5. Conti..
 BLAST is the tool for finding sequence similarity to the query sequence. It
searches query sequence from NCBI database
 NCBI-BLAST results can be represented in graphical format
 HTML is the default output format of NCBI webpage
 Enterz is cross database search system used at NCBI for all major
databases such as DNA, protein sequences, protein structure, Pubmed,
OMIM. Etc
 NCBI distributes first version of Enterz in 1991
 NCBI has implement ‘Gene’ to characterise and organise into about gene
 It serves major nodes in Texas of genomic map, expression, sequence
finding etc.
 NCBI has imported 3D structures in PDB
 Pubchem database is a public resource of molecule and their activities in
NCBI

8. EMBL
 EMBL ( European Molecular Biology Laboratory )
 It is a nucleotide sequence database created in 1974
 It is a molecular biology research institute
 http::// WWW.ebi.ac.uk/embl/index.html
 It was maintained by EBI( European Bioinformtics institute ) in an
international collaboration with DDBJ and Gen Bank
 Data exchanged among collaborated database on daily basis
 Individual authors and genome projects groups are the major
source of information for EMBL
 Many sequence similarity searching tools are available in EMBL

12. DDBJ
 DDBJ( DNA Data bank of Japan )
 It is a biological database that collect DNA sequencing
 Located at national institute of genetics ( NIG) in Japan
 It was functioned first in 1986
 They receive information from Japanese researchers
 they were funded by Ministry of education, Culture, Science and
technology of Japan (MEXT)
 They collect nucleotide sequence data as a member of INSDC(
International Nucleotide Sequence Database Collaboration)
 The information collected various source in DDBJ are freely
accessible for researchers

16. PROTEIN DATA BANKS
 The Protein Data Bank (PDB) is a database for the three-dimensional
structural data of large biological molecules, such as proteins and nucleic
acids
 PDB has three official branches: the Research Collaboratory for Structural
Bioinformatics (RCSB, USA), the European Bioinformatics Institute
(PDBe, UK), and the Protein Data Bank Japan (PDBj, Osaka).
 PDB access is provided through primary web and ftp sites (www.pdb.org,
ftp.pdb.org) or via multiple mirror sites distributed worldwide.
 The Protein Data Bank (PDB) was established in 1971 with fewer than ten
X-ray crystallographic structures of proteins, becoming the first open
access digital data resource in the biological sciences
 The Protein Data Bank (pdb) file format is a textual file format describing
the three-dimensional structures of molecules held in the Protein Data
Bank.

17. Conti ….
 The Protein Data Bank (PDB) archive is the single worldwide repository
of information about the 3D structures of large biological molecules,
including proteins and nucleic acids.
 The RCSB PDB has an international community of users, including
biologists (in fields such as structural biology, biochemistry, genetics,
pharmacology)
 Other scientists (in fields such as bioinformatics, software developers for
data analysis and visualization)
 Students and educators (all levels); media writers, illustrators, textbook
authors; and the general public.
 The RCSB PDB Advisory Committee is made up of an international team
of experts in X-ray crystallography, cryoEM, NMR, bioinformatics and
education. RCSB PDB appreciates the valuable feedback they provide on
an ongoing basis.

21. Swiss –prot
 Universal protein resources knowledge base (Uniprot) is the central
hub for the collection of functional information of protein
 Swiss-prot is mainly annotated and received section of Uniprot
 It was established in 1986
 And maintained by Swiss institute for Bioinformatics and EBI
 They provide protein sequence database that provide a high level
of annotation, minimal redundancy and integration with other
database
 Data can be diffentiated into two types core and annotation data
 Core contains citation informations that is bibliographic reference
and taxonomic information that is biological source of protein
 Annotation data contains function of protein, post translational
modification, Domains and sites, secondary structure, quaternary
structure and disease associated

22. Minimal redundancy
 Much of the data comes from more than one literature report
 Data condensed and merged to appear more concise and coherent
 Conflicts in data are listed for each entry
Integration with other data
 Swiss –prot provides cross reference to external data collection
 Integration between the three types of sequence related database( nucleic
acid sequence, protein sequence and protein tertiary structure)

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