1. Database
A Computerized archive used to store and organize data in such
a way that information can be retrieved easily.
A database is a repository of information that has a specific
structure that enables the entering and extraction of data
In general this database structure consists of files or tables,
each containing numerous records and fields
2. Conti..
Database System (DBS) is an integrated collection of related files
along with the detail about their definition, interpretation,
manipulation and maintenance
A database system is based on the data. Also a database system can
be run or executed by using software called DBMS (Database
Management System).
A database system controls the data from unauthorized access.
A database management system (DBMS) is a collection of programs
that enables users to create and maintain a database.
3. Database management systems
Database management systems provide several functions in
addition to simple file management:
control security
maintain data integrity
provide for backup and recovery
control redundancy
allow data independence
provide non-procedural query language
perform automatic query optimization
4. Organisation
Organisation:
flat files
Relational databases
Flat-file databases
the simplest form of a database,
where collections of data, such as nucleotide and amino
acid sequence, are stored as either a large single text file
6. Conti..
a database that treats all of its data as a collection of
relations
A relational database stores the data within a number of
tables.
Each table consists of records and fields (rows and
columns)
7. Types of Database
The databases can be classified into three
categories on the basis of the information
stored.
They are Primary, Secondary and
Composite databases.
Primary databases contain data that is
derived experimentally.
They usually store information related to
the sequences or structures of biological
components
They can be further divided into protein or
nucleotide databases
8. Primary Database
This databases contains the raw nucleic acid sequence data
which are produced and submitted by researchers worldwide.
NCBI(The National Centre for Biotechnology Information)
GenBank
DDBJ (DNA data bank of Japan)
SWISS-PROT(Swiss-Prot )
PIR (Protein Information Resource)
PDB(Protein Data Bank)
TrEMBL (Translated European Molecular Biology Laboratory)
Protein
PIR
MIPS
SWISS-PROT
TrEMBL
10. Secondary Databases
Secondary Databases:
contain information derived from primary databases.
store information such as conserved sequences, active
site residues, and signature sequences. Protein
Databank data is stored in secondary databases.
Examples include:
Class Architecture Topology Homology (CATH),
Kyoto Encyclopedia of Genes and Genomics (KEGG),
Protein Families (Pfam)
and Structural Classification of Proteins (SCOP)
11. Composite Databases
Composite Databases
are collections of several primary database resources.
provide users with various tools and software for analysis of data.
NCBI being a composite database has stored a lot of sequence of
nucleotide and protein within its server and thereby suffers from
high redundancy in the data deposited
12. Biological databases
Biological databases can be broadly classified in to
Sequence database
structure database
and pathway databases.
Sequence databases are applicable to both nucleic acid sequences
and protein sequences, whereas structure databases are applicable
to only Proteins.
13. Sequence databases
Sequence databases
Nucleotide and protein sequence databases represent the most
widely used and some of the best established biological
databases.
serve as repositories for wet lab results and the primary source
for experimental results.
Major public data banks included in this type are
GenBank in USA,
EMBL (European Molecular Biology Laboratory) in Europe
and DDBJ (DNADataBank) in Japan
14. Conti….
And protein databases includes
ExPaSy
UniProt
PIR
PDB
Swiss-Prot
TrEMBL
15. NATIONAL CENTER FOR BIOTECHNOLOGY
INFORMATION (NCBI)
developed at the National Institutes of Health (NIH) in 1988
Part of national library of medicine at national institute of
health
provides access to a large amount of biomedical and genomic
information (www.ncbi.nlm.nih.gov/home/
about/mission.shtml).
It maintains a large scale of databases and bioinformatics
tools as well as services.
One of the most popular databases is GenBank
16. Conti…
Mission or role
The aim is to find novel techniques and methodologies for dealing
with huge and complex data
and provide better accessibility to analytical and computational
tools.
Maintenance of biological databases whether primary or
secondary.
It includes GENEBANK
NCBI provides the data retrieval systems such as ENTREZ
Provides computational sources for the analysis of the GENEBANK
data and other biological data
17. Conti…
Resources
The resources that are present on this site can be divided
into two major categories:
1) databases
2) tools
18. The major databases maintained at NCBI are
GenBank and PubMed (bibliographic database for biomedical literature).
Other databases include the
Gene,
Genome,
Epigenomics,
Gene
Expression
RefSeq,
Structure, Database of Short Genetic Variation (dbSNP),
TAXONOMY, etc.
19. TOOLS at NCBI
The NCBI also provides a variety of tools for database search
The Entrez: is search engine of NCBI
The other tools include
Genomes Browser,
BLAST,
CDTree,
Genetic Codes,
Open Reading Frame Finder (ORF Finder),
SNP Database Specialized Search Tools,
20. GenBank
GenBank (Genetic Sequence Databank)
GenBank® is the genetic sequence database at the National Center for
Biotechnology Information (NCBI).
It was established in the year 1982 and now maintained by the
National Center for Biotechnology (NCBI).
It contains publicly available nucleotide sequences
DNA sequences can be submitted to GenBank using several different
methods.
BankIt: Web-based form for submission of a small number of
sequences
Sequin: More appropriate for complicated submissions containing
many sequences
21. Structure of Genbank
A detailed structure of a nucleotide
sequence file format in this database
includes the following:
1. Locus: This can be defined as a title
given by GenBank itself to name the
sequence entry. It includes the
following:
a. Locus Name: Similar to accession
number for the sequence.
b. Sequence Length: Tells the number
of bases existing in the sequence.
22. Conti….
c. Molecule-Type: Identifies the
type of nucleic acid sequence.
The various types are mRNA
(which is present as cDNA), rRNA,
snRNA, and DNA.
d. GB Division: Postulates class of
the data according to
classification criteria of GenBank.
e. Modification Date: The date on
which the record was modified.
23. 2. Definition: This denotes the name of the
nucleotide sequence.
3. Accession: This covers accession number,
accession version, and GI number.
Accession number can be defined as the
unique identifier associated with each
nucleotide sequence present in the
database.
4. VERSION - Identification number assigned
to a single, specific sequence in the
database. This number is in the format
“accession.version.”
5. GI Also a sequence identification
number. Whenever a sequence is changed,
the version number is increased and a new
GI is assigned.
24. 6. Keyword: Defined words that
were used to index the entries.
7. The Source: This describes
organism from which sequences
have been obtained.
8. Organism - The scientific name
(usually genus and species) and
phylogenetic lineage
9. REFERENCE - Citations of
publications by sequence authors,
the journal from which with the
sequence was derived
25. 10. Features: These
consist of the
information derived
from the sequence
such as biological
source,
exon,
intron,
promoters,
CDS
alternate splice,
Base Count,
Origin
26. European Molecular Biology Laboratory
(EMBL)
The EMBL Nucleotide Sequence Database is maintained by EBI,
UK
It was formed in the year 1974
It develops and maintains a large number of databases, and
scientists can access the data free of cost.
This database serves as the primary source of nucleotide
sequences for Europe.
in this database, the nucleotide sequence data generated by
large-scale genome-sequencing projects and those available
from the European Patent Office can be submitted
27. Conti…
Data collection is done in collaboration with GenBank
(USA) and the DNA Database of Japan (DDBJ).
The other genomic databases held at EBI are
Ensembl (a database of genome annotation)
Genome Reviews.
The daily releases of the database contain new
submissions and updated sequence data
while every 3 months the entire database is released.
28. DDBJ
DDBJ: DNA Data Bank of Japan Is a biological database
that collects DNA sequences submitted by researchers.
It is run by the National Institute of Genetics, Japan.
DDBJ Flat File Format
The data submitted in DDBJ is managed and retrieved
according to the DDBJ format (flat file).
The flat file includes the sequence and the information of
who submitted the data, references, source organisms,
and information about the feature, etc
29. Ensembl Genome Database
Ensembl is one of several well known genome browsers for the
retrieval of genomic information from several organisms
including human, plants, bacteria and animals.
Created and maintained by the EBI and the Sanger Center (UK)
30. databases for green plants
There are three different comparative genomic databases
for green plants, namely,
GreenPhylDB,
Plaza,
Phytozome
These databases aim to support studies on genomics
studies related to plant evolution and
to provides comparative data on genomes and gene
families and the tools for their analysis.
31. Conti…..
It provides information on
genomic context of plant genes,
Gene homologues, and paralogues,
RNA transcripts from the given genes,
peptide sequences, and
functions of gene families.
It allows access to complete genome sequences available in the
database.
32. Protein Databases
Swiss-Prot
Swiss-Prot is a protein sequence and knowledge database.
It is well known for high quality of annotation, use of
standardized nomenclature, and links to specialized databases.
its repository contains the amino acid sequence, the protein
name and description, taxonomic data, and citation information
PFAM
A database of protein families, Pfam contains annotations as
well as multiple sequence alignments generated using hidden
Markov models
33. Conti…
TrEMBL: The European Bioinformatics Institute, collaborating with
Swiss-Prot, introduced another database, TrEMBL (translation of EMBL
nucleotide sequence database)
This database consists of computer annotated entries obtained from
the translation of all coding sequences in the nucleotide databases.
PIR: The Protein Information Resource (PIR) is an integrated public
bioinformatics resource that supports genomic and proteomic
research and scientific studies
The PIR serves the scientific community through on-line access, and
performing off-line sequence identification services for researchers.
It is a database of freely accessible protein sequences which contains
high-quality data and functional information for the proteins
34. Structure databases
There are many structural database that include
Protein DataBank (PDB)
Important in solving real problems in molecular biology
PDB Established in 1972 at Brookhaven National
Laboratory (BNL)
It contains structural information of the macromolecules
determined by X-ray, crystallographic, NMR methods
PDB is maintained by the Research Collaboratory for
Structural Bioinformatics (RCSB).
35. Conti…
PROSITE: is a database of protein domains and families.
PROSITE contains biologically significant sites, patterns
and profiles that help to reliably identify to which known
protein family a new sequence belongs.
CATH: The CATH database (Class, architecure, topology,
homologous superfamily) is a hierarchical classification of
protein domain structures, which clusters proteins at four
major structural levels.
36. Pathway databases
Pathway databases
A pathway database (DB) is a DB that describes
biochemical pathways, reactions, and enzymes
Some examples of the pathway databases are
KEGG (The Kyoto Encyclopedia of Genes and Genomes)
BRENDA,
Biocyc.
37. Conti…
KEGG: The Kyoto Encyclopedia of Genes and Genomes (KEGG) is the
primary resource for the Japanese Genome Net service
it is a collection of online databases dealing with genomes, enzymatic
pathways, and biological chemicals
KEGG contains three databases: PATHWAY, GENES, and LIGAND.
The PATHWAY database stores computerized knowledge on molecular
interaction networks.
The GENES database contains data concerning sequences of genes and
proteins generated by the genome projects.
The LIGAND database holds information about the chemical compounds and
chemical reactions that are relevant to cellular processes.
38. BioCyc: The BioCyc Database Collection is a compilation of
pathway and genome information for different organisms.
It includes two other databases,
EcoCyc which describes Escherichia coli K-12;
MetaCyc, which describes pathways for more than 300
organisms.