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3 Database

A database is a computerized archive used to store and organize data in such a way that
information can be retrieved easily via a variety of search criteria.

Databases are composed of computer hardware and software for data management.
The chief objective of the development of a database is to organize data in a set of
structured records to enable easy retrieval of information.

Types of databases
• Originally, databases all used a flat file format, which is a long text file that contains
many entries separated by a delimiter, a special character such as a vertical bar (|).
Within each entry are a number of fields separated by tabs or commas.
• To facilitate the access and retrieval of data, sophisticated computer software
programs for organizing, searching, and accessing data have been developed. They
are called database management systems.

Biological databases
Based on their contents, biological databases can be roughly divided into four categories:
primary databases, secondary databases, specialized databases and composite databases

Example. A few popular databases are GenBank from NCBI (National Center for
Biotechnology Information), SwissProt from the Swiss Institute of Bioinformatics and PIR
from the Protein Information Resource.

1. Primary databases
 Primary databases are also called as archieval database.
 They are populated with experimentally derived data such as nucleotide sequence,
protein sequence or macromolecular structure.
 Experimental results are submitted directly into the database by researchers, and the
data are essentially archival in nature.
 Once given a database accession number, the data in primary databases are never
changed: they form part of the scientific record.
Examples
Swiss-Prot and PIR for protein sequences
GenBank and DDBJ for genome sequences
Protein Databank (PDB) for protein structures

2. Secondary databases
 Secondary databases comprise data derived from the results of analysing primary
data.
 Secondary databases often draw upon information from numerous sources,
including other databases (primary and secondary), controlled vocabularies and the
scientific literature.
 They are highly curated, often using a complex combination of computational
algorithms and manual analysis and interpretation to derive new knowledge from
the public record of science.

Bioinformatics collected by Dr. Nawab Ali Assistant Prof. GDC Thana, District Malakand 1
 Examples
InterPro (protein families, motifs and domains)
UniProt Knowledgebase (sequence and functional information on proteins)
Ensembl (variation, function, regulation and more layered onto whole genome
sequences)
SWISS-Prot and Protein Information Resources (PIR)

Some of the common secondary databases include:

i) Prosite
 It was the first secondary database developed.
 Protein families usually contain some most conserved motifs which can be encoded
to find out various biological functions.
ii) Prints
 Most protein families are characterized by several conserved motifs.
 All of these motifs can be an aid in constructing the `signatures’ of different families.
This principle is highlighted in constructing PRINT database.
 PROSITE and PRINTS are the only manually annotated secondary databases. The
print is a diagnostic collection of protein fingerprints.
iii) Blocks
 The limitations of the above two databases led to the formation of Block database.
 In this database, the motifs (here called Blocks) are created automatically by
highlighting and detecting the most conserved regions of each family of proteins.
 Blocks are ungapped Multiple Sequence Alignment representing conserved protein
regions.
iv) Profiles
 Profile database is used to find out the most conserved regions in the sequence
alignment. The profile is weighted to indicate modifications (in bioinformatics called
INDELS) are allowed in the sequence.

3) Specialized databases
There are also specialized databases are those that cater to a particular research
interest. For example, Flybase, HIV sequence database, and Ribosomal Database Project are
databases that specialize in a particular organism or a particular type of data.

4) Composite databases
It contain a variety of primary databases, which eliminates the need to search each
one separately. Each composite database has different search algorithms and data structures.
The NCBI hosts these databases, where links to the Online Mendelian Inheritance in Man
(OMIM) is found.

Importance of Databases
1. Databases act as a store house of information.
2. Databases are used to store and organize data in such a way that information
can be retrieved easily via a variety of search criteria.
3. It allows knowledge discovery, which refers to the identification of
connections between pieces of information that were not known when the

Bioinformatics collected by Dr. Nawab Ali Assistant Prof. GDC Thana, District Malakand 2
 information was first entered. This facilitates the discovery of new biological
insights from raw data.
4. Secondary databases have become the molecular biologist’s reference library
over the past decade or so, providing a wealth of information on just about
any gene or gene product that has been investigated by the research
community.
5. It helps to solve cases where many users want to access the same entries of
data.
6. It helps to remove redundancy of data.

A list of some frequently used databases is provided in Table 2.1.

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Nucleic acid sequence databases
The Nucleotide database is a collection of sequences from several sources, including
GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the
foundation for biomedical research and discovery.

1. Primary databases of nucleotide sequences

 There are three chief databases that store and make available raw nucleic acid
sequences to the public and researchers alike: GenBank, EMBL, DDBJ.
 They are referred to as the primary nucleotide sequence databases since they are the
repository of all nucleic acid sequences.
 GenBank is physically located in the USA and is accessible through the NCBI portal
over the intern. This database is produced and maintained by the National Center for
Biotechnology Information (NCBI)
 EMBL (European Molecular Biology Laboratory) is in UK
 DDJB (DNA databank of Japan) is in Japan. It is the only nucleotide sequence data
bank in Asia. Although DDBJ mainly receives its data from Japanese researchers, it
can accept data from contributors from any other country.

2. Secondary databases of nucleotide sequences

 Many of the secondary databases are simply sub-collection of sequences culled from
one or the other of the primary databases such as GenBank or EMBL.
 There are other secondary databases that do not present sequences at all, but only
information gathered from sequences databases.
Examples:
i) Omniome Database:
Omniome Database is a comprehensive microbial resource maintained by TIGR (The
Institute for Genomic Research).
ii) FlyBase Database:
A consortium sequenced the entire genome of the fruit fly D. Melanogaster to a high degree
of completeness and quality.
iii) ACeDB:
It is a repository of not only the sequence but also the genetic map as well as phenotypic
information about the C. Elegans nematode worm.

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Protein databases
 The biological information of proteins is available as sequences and structures.
Sequences are represented in a single dimension whereas the structure contains the
three-dimensional data of sequences.
 A protein database is one or more datasets about proteins, which could include
a protein’s amino acid sequence, conformation, structure, and features such as active
sites.
 Protein databases are compiled by the translation of DNA sequences from different
gene databases and include structural information. They are an important resource
because proteins mediate most biological functions.
Importance of protein databases
Huge amounts of data for protein structures, functions, and particularly sequences are being
generated. Searching databases are often the first step in the study of a new protein. It has
the following uses:
1. Comparison between proteins or between protein families provides information
about the relationship between proteins within a genome or across different species
and hence offers much more information that can be obtained by studying only an
isolated protein.
2. Secondary databases derived from experimental databases are also widely available.
These databases reorganize and annotate the data or provide predictions.
3. The use of multiple databases often helps researchers understand the structure and
function of a protein.

Primary databases of protein

The PRIMARY databases hold the experimentally determined protein sequences inferred
from the conceptual translation of the nucleotide sequences. This, of course, is not
experimentally derived information, but has arisen as a result of interpretation of the
nucleotide sequence information and consequently must be treated as potentially containing
misinterpreted information. There is a number of primary protein sequence databases and
each requires some specific consideration.
a. Protein Information Resource (PIR) – Protein Sequence Database (PIR-PSD):
b. SWISS-PROT
c. Protein Databank (PDB):
Secondary databases of proteins
The secondary databases are so termed because they contain the results of analysis of the
sequences held in primary databases. Many secondary protein databases are the result of
looking for features that relate different proteins. Some commonly used secondary databases
of sequence and structure are as follows:
a. PROSITE:
b. PRINTS:
c. MHCPep:
d. Pfam

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