Databases

Dr. Shazia Rehman

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
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Database System (DBS) is an integrated collection of related files along with the
detail about their definition, interpretation, manipulation and maintenance
A database system controls the data from unauthorized access.
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
perform automatic query optimization
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
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A relational database stores the data within a number of tables.
Each table consists of records and fields (rows and columns)
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
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)
Protein
SWISS-PROT(Swiss-Prot ) PIR
PIR (Protein Information Resource) MIPS
PDB(Protein Data Bank) SWISS-PROT
TrEMBL (Translated European Molecular Biology TrEMBL
Laboratory)
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 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)
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
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.
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
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And protein databases includes
ExPaSy
UniProt
PIR
PDB
Swiss-Prot
TrEMBL
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
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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
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Resources
The resources that are present on this site can be divided into two major
categories:
1) databases
2) tools
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.
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,
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
 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.
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• 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.
• 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.
• 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
 10. Features: These
consist of the
information derived
from the sequence such
as biological source,
 exon,
 intron,
 promoters,
 CDS
 alternate splice,
 Base Count,
 Origin
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
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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.
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
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)
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.
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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.
Protein Databases
Swiss-Prot
• A protein sequence database which strives to provide a high level of annotation:
* the function of a protein
* domains structure
* post-translational modifications
* variants
• Complete, Curated, Non-redundant and cross-referenced with 34 other 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
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TrEMBL: TrEMBL (translation of EMBL nucleotide sequence database) was

introduced by the European Bioinformatics Institute in collaborating with Swiss-Prot
• Created in 1996 as a computer annotated supplement to SWISS-PROT.
• Contains translations of all coding sequences (CDS) in EMBL.
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
Structure databases
There are many structural database that include
Protein Data Bank (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).
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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.
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.
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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.
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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.