Introduction to

bioinformatics
(databases)
Course Code –BOTY 4204
Course Title- Techniques in plant sciences , biostatistics and
bioinformatics

By – Dr. Alok Kumar Shrivastava

Department of Botany
Mahatma Gandhi Central
University, Motihari
 What is bioinformatics ?
• In biology, bioinformatics is defined as, “the use
of computer to store, retrieve, analyse or predict
the composition or structure of bio-molecules” .
Bioinformatics is the application of
computational techniques and information technology
to the organisation and management of biological
data. Classical bioinformatics deals primarily with
sequence analysis.
 Aims of bioinformatics
 Development of database containing all
biological information.
 Development of better tools for data designing,
annotation and mining.
 Design and development of drugs by using
simulation software.
 Design and development of software tools for protein
structure prediction function, annotation and docking
analysis.
 Creation and development of software to improve tools
for analysing sequences for their function and similarity
with other sequences
 Applications of bioinformatics

Crop Antibiotic
development resistance
Gene
therapy

Drought
resistance
Drug
designing

Applications of
Forensic
bioinformatis
analysis
Medicine
biotechnology

Wheather
analysisy
Evolutionary
studies
Waste Veterinary
ceanup science
 Biological databases
• Biological data are complex, exception-ridden, vast
and incomplete. Therefore several databases has been
created and interpreted to ensure
unambiguous results. A collection of biological
data arranged in computer readable form that
enhances the speed of search and retrieval and
convenient to use is called biological database.
A good database must have updated
information.
 Importance of biological database
•A range of information like biological
sequences, structures, binding sites, metabolic
interactions, molecular action, functional
relationships, protein families, motifs and
homologous can be retrieved by using biological
databases. The main purpose of a biological database
is to store and manage biological data and
information in computer readable forms.
 Types of biological
database
Primary secondary
database Derived
database database

Nucleotide Protein structur Domain and

Protein databas e
sequence database sequence motif database
e Prosite
database PDB
Gene Swis-port
bank EBI-MSD
Blocks
DDBJ PIR MMDB
COG
EMBL
GenePept
Structure Gen Metaboli Specialised
database expression cpathway database
database databas
SCOP TGI
e KEGG
GEOGXD GSOB
CATH PathD
GPCRD
B
 Primary database vs. secondary
database
• A primary database contains only sequence or
structural information.
• The database derived from the analysis or treatment of
primary data are secondary database. It is very
important for interfering protein function.
Examples of some primary
biological database
 GeneBan
 One of the fastest growingkrepositories of known nucleotide sequences,
GeneBank (Genetic Sequence Databank), has a flat file structure. It is an
ASCII text file, readable by both humans and computers. Besides sequence
data, GeneBank files contain information such as accession numbers and
gene names, phylogenetic classification and references to published literature.

 This database has been developed and maintained at the NCBI, Bethesda,
MD,
USA, as a part of International Sequence Database Collaboration (INSDC).

 It is an open access sequence database.

 It coordinates with individual and other sequence databases
laboratories EMBL and DDBJ. like

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 It is an annotated collection of all nucleotide sequences that are
available to the public.

 The nucleotide database was divided into three databases at

NCBI: CoreNucleotide database, Expressed Sequence Tag (EST) and
Genome Survey Sequence (GSS).

 CoreNucleotide database has most of the nucleotide sequences used. It

also encloses all nucleotide records that are not in the EST and GSS
databases.

 Submission of sequences to GeneBank can be done using BankIt,

Sequin and tbl2asn tools.
 EMBL(European Molecular
Biology Laboratory)
• A comprehensive database of DNA and RNA sequences,
EMBL nucleotide sequence database is collected from scientific
literature, patient offices and is directly submitted by
researchers. EMBL has been prepared in collaboration
with GeneBank (USA) and the DNA Database of Japan
(DDBJ).
• It is established in 1980.
• It is maintained by EBI (European Bioinformatics Institute)
 Swiss-
 This is a curated protein sequence database that offers a high
Port
level of integration with other databases and also has a very
low level of redundancy. Swiss-Port strives to provide protein
sequences with a high level of annotation (for instance, the
description of protein function, domain structure and post
translational modifications, etc.).
 It is established in 1986 and maintained collaboratively ,
since 1987, by the department of Medical Biochemistry
of the University of Geneva and the EMBL data Library.
 TrEMBL is a computer–annotated supplement of Swiss-Port
that contains all translations of EMBL nucleotide sequence
entries, which is not yet integrated in Swiss-Port.
 Currently Swiss-Port have 0.5 and TrEMBL have 7.6
milliom sequences.
 Protein Information Resource(PIR)
• PIR is an integrated public bioinformatics resource
to support genomic and proteomic research and
scientific studies. Nowadays, PIR offers a wide
variety of resources mainly oriented to
assisting the propagation and consistency of
protein annotations like PIRSF, ProClass and
ProLINK.
Examples of Some Secondary
Biological Database
 Motif Databases
• Protein sequence motif is a set of conserved amino
acid residues that are important for protein function and are
located within a certain distance from one another.
These motifs usually provide clues to the functions
of otherwise uncharacterised proteins.
• The PROSITE database consists of documentation
entries describing protein domains, families and functional
sites as well as associated patterns and profiles to identify
them.
• PRINT is a database for protein fingerprints. A fingerprint is
a group of conserved motifs used to characterise a
protein family.
 Domain Database
• A protein domain is an independently folded,
structurally compact unit that forms a steady three-
dimensional structure and shows a certain level of
evolutionary conservation. Typically , a conserved domain
contains one or more motifs.
• ProDom is a protein domain database automatically
generated from the Swiss-Port and TrEMBL sequence
database.
• SMART is a highlyreliableand sensitive tool for
domain identification.
• COG is a database and a convenient tool for motif and
domain identification.
 3D Structure databases
• PDB (Protein Data bank) is the main primary database for
3D structures of biological macromolecules determined by
X-ray, crystallography and NMR. It also accepts
experimental data used to determine the structures and
homology models.
• SCOP (Structural Classification of Protein database)
classifies protein 3D structures in a hierarchical scheme
of structure classes. All the protein structures in PDB are
classified her, and the updated new structures are deposited
in PDB.
• The CATH database (Class, Architecture, Topology,
Homologous) contains a hierarchical classification of
protein domain structure.
 Protein data bank

• PDB (Protein data bank) is a repository for 3D

structural data obtained by x-ray
crystallography or NMR spectroscopy of
proteins and nucleic acids.
• Research Collaboratory for Structural
Bioinformatics (RCSB) PDB provides a variety of
tools and resources for studying the structures of
biological macromolecules and their relationship with
other sequences, its function and diseases caused
if any .
 Gene expression databases
• GEO or Gene Expression Omnibus is a curated
online resource and a gene expression molecular
abundance repository for gene expression data browsing,
query and retrieval.
• GXD or Gene Expression Database is a community
resource for gene expression information.
• MGED or Microarray Gene Expression data
contains microarray data, generated by functional
genomics and proteomics experiments.
• ArrayExpress from European Bioinformatics Institute is
a repository for transcriptomics data.
 Metabolic pathway databases
• KEGG PATHWAY Database contains graphical pathway maps
for all known metabolic pathways from various organisms.
• EcoCyc is an E. coli database , stores information regarding
the genome and biochemical machinery of E. coli.
• LIGAND is a chemical database for enzyme reactions at the
Institute for Chemical Research, Kyoto. It is composite database
currently consisting of the COMPOUND, DRUG, GLYCAN,
REACTION, RPAIR and ENZYME databases.
• MetaCyc is a non-redundant, experimentally elucidated
metabolic pathway database.
• BRENDA is an enzyme database tat contains information on
all aspects of enzymes and enzymatic reactions.
 Genome databases
• Genome databases give absolute information on the
heritable properties of an organism. These databases help
to identify genes and predict their functions. A few
genome databases have links with specific organism
databases.
• GOLD (Genomes Online Database at the University
of Illinois, USA) contains a list of all the complete and
ongoing genome projects worldwide.
• Genomes at NCBI (National Centre for
Biotechnology Information, USA).
• TIGR database (TDB), at the institute for Genomic
Research at Rockeville MD, USA.
 Virological databases
• A virological database contains all the sequences
and related information of viruses of animals, plants,
bacteria,and archea; for example,
fungi HIV
the
database. A committee called protease
The ee on Taxonomy of Viruses(ICTV)
Committ International
authorises and organises the taxonomic classification
of viruses. ICTVdB contains taxonomic information
for over thousands of virus species.
 World biodiversity databases
• Taxonomic databases are builtto document all
known
species make them available accessible
and
worldwide. These and
databases contain
hierarchies, specie names,
taxonomic descriptions,
illustrations and
s references.
synonyms,For example: CCINFO,
STRAIN and
ALGAE.
 Database for various model
organismscoli- E. coli Genome Centre(Wisconsin
• Escherichia
university, USA), The E.coli index (University of Birmingham, UK)
• Arabidopsis thaliana- TAIR (The Arabidopsis Information
Resource)
• Homo sapiens- Human Genome Resources at NCBI, USA
• oryza sativa(rice) -RGP (Rice Genome Research
Programme, Japan)
• Drosaphila melanogaster -FlyBase (Drosophila Genome Database)
• Mus musculus (mouce)- Mouce Genome Informatics
• Danio rerio(zebrafish)- ZFIN (Zebrafish Information Network at
the University of Oregon, USA)
• S. cerevisiae (Bakersyeast)-SGD ()Yeast Genome Database
 Annotation of
Genegenomes
In molecular biology, ????? make the basic genetic material
and typically consist of DNA. Whereby, genome include the genes
(coding ) and non coding regions, of interest to us, are the coding
regions as they actively influence basic life processes. The
genes contain useful biological information that is required in
building up and maintaining an organism. Gene annotation can be
defined merely as the process of making nucleotide sequence
meaningful.
Gene annotation involves the process of taking the raw DNA
sequence produced by genome sequencing projects and adding layers
of analysis and interpretation necessary to extracting
biologically significant information and placing such derived details
into context. Annotation is the process by which pertinent
 Accession number

Accession numbers are unique identifiers

which permanently identify sequences in the
database. Accession numbers are
assigned and communicated to authors within
two working days of the receipt of submission.