What is Bioinformatics?

Bioinformatics is a subject that is a combination of biology

and technology. It requires complete knowledge of
engineering as well as life sciences. This sector draws from a
well of biological data and uses this information to create new
tools and software which will be possible in the area of
biological research. Bioinformatics is subdivided into two
sections, namely,

• Animal bioinformatics
• Plant bioinformatics

Bioinformatics

Applications of Bioinformatics

Bioinformatics and its application depend on taking out useful

facts and figures from a collection of data reserved to be
processed into useful information. Bioinformatics focuses its
scope on the areas of 3D image processing, 3D modeling of
living cells, image analysis, drug development, and a lot more.
The most important application of bioinformatics can be seen in
the field of medicine, where its data is used to create antidotes
for infectious and harmful diseases.
The main applications of bioinformatics is to make the complete
use of natural processes more usable and less complicated.

Some examples of the application of bioinformatics are as

follows –

• Bioinformatics is largely used in gene therapy.

• This branch finds application in evolutionary concepts.
• Microbial analysis and computing.
• Understanding protein structure and modeling.
• Storage and retrieval of biotechnological data.
• In the finding of new drugs.
• In agriculture to understand crop patterns, pest control,
and crop management.

Applications of Bioinformatics
Bioinformatics: A Definition
History of Bioinformatics
• Bioinformatics is the application of computer science and
information technology to the field of biology. It involves
the use of algorithms to analyze biological data, such as
DNA sequences, in order to understand how they work
and how they evolved. Bioinformatics also involves the
use of databases to store this data, as well as software
tools to help researchers explore and analyze it.
• The field of bioinformatics emerged in the early 1990s,
when researchers began to use computers to sequence
DNA. At the time, there was no standardized way to store
and analyze this data, so early bioinformatics tools were
often quite primitive. However, the field has progressed
rapidly in recent years, and there are now a number of
sophisticated bioinformatics tools available to researchers.
These tools are used to study everything from the human
genome to the genomes of other species.
• Bioinformatics is playing an increasingly important role in
modern biology. It is used to help researchers understand
how genes work, how proteins are made, and how viruses
evolve. Bioinformatics is also being used to develop new
drugs and treatments for diseases.

Application of Bioinformatics in medicine

Bioinformatics is the application of computer science and
information technology to the field of biology. It is a
interdisciplinary field that develops methods and software tools
for understanding biological data. Bioinformatics has been used
in medicine for many years to help researchers understand the
genetic basis of diseases. Bioinformatics tools are also used to
develop new drugs and to improve the diagnosis and treatment
of diseases.
Bioinformatics Applications List
There are many different applications of bioinformatics. Some
of the most common ones are listed below.

• Sequence alignment – This is the process of aligning two

or more sequences of DNA or protein to identify regions of
similarity. This can be used to identify shared genetic
sequences, to determine the evolutionary relationships
between different species, and to find new drug targets.
• Sequence analysis – This is the process of examining the
sequence of DNA or protein to identify features such as
genes, regulatory elements, and protein domains. This
information can be used to study the function of genes
and proteins and to identify potential drug targets.
• Gene expression analysis – This is the process of
measuring the levels of gene expression in different cells
or tissues. This can be used to identify different types of
cells, to study the function of genes, and to identify
potential drug targets.
• Genome sequencing – This is the process of sequencing
the entire genome of a species. This can be used to study
the genetic makeup of a species, to identify genes and
genetic variants, and to study the evolutionary
relationships between different species.
• Transcriptome sequencing – This is the process of
sequencing the transcriptomes of different cells or tissues.
This can be used to identify different types of cells, to
study the function of genes, and to identify potential drug
targets.
• Proteome sequencing – This is the process of sequencing
the proteomes of different cells

The roles of bioinformatics

One of the main tools created by bioinformatics was databases.
Several hundred databases hold different types of biological data
like complete genomes and gene sequences. Databases allow
the data to be stored and searched logically, enabling
comparisons and links to be made that would have otherwise
escaped the naked eye. These databases have increasing amounts
of data that are growing at an exponential rate as we sequence
more DNA.

When comparing genomes present in these databases, sequence

similarity can be assessed. Increasing DNA sequence similarity
is indicative of recent common ancestry. These tools allow us
to build evolutionary trees and see how life relates to each
other because knowing the basic mutation rate of DNA and how
similar two sequences/genomes are, we can infer when two
genetic sequences from different species diverged from a common
ancestor.

Popular bioinformatics databases include

the Ensembl database, which holds genomes of eukaryotic
organisms like the human genome. Ensembl also includes the
genomes of other important model organisms like the zebrafish,
house mouse or the fruit fly. Other popular databases
include GenBank and DDBJ.

The BLAST (Basic Local Alignment Search Tool) tool is one of

bioinformatics most relevant software algorithms used today. The
BLAST tool allows researchers to compare millions of primary
biological sequences present in the database with minimal
effort. These comparisons help find sequence
similarities amongst unknown sequences researchers are
studying with those already present in the database.
As our knowledge of the DNA coding sequencing of living organisms’
genomes grew through DNA sequencing, so did our knowledge of
what it codes: proteins. Knowing the genetic code of life, we
can decipher what a gene encodes, meaning the protein
its transcription and translation might result in. Databases were also
created to contain the resulting amino acid sequences
of proteins and protein structures, like UniProt (Universal protein
resource). UniProt contains various amino acid sequence data
alongside its respective protein function.

Bioinformatics is closely related to another emergent field in

bioscience known as computational biology. The bioinformatics
field created the computational biology field. Whereas bioinformatics
collects and processes vast amounts of biodata, computational
biology uses such data to construct theoretical models of
biological systems. These models try to predict, for example, 3D
structures of proteins or help identify specific genes linked to
diseases in populations.

Scope of Bioinformatics

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The main scope of Bioinformatics is to fetch all the
relevant data and process it into useful information. It
also deals with –
• Management and analysis of a wide set of
biological data.
• It is specially used in human genome sequencing
where large sets of data are being handled.
• Bioinformatics plays a major role in the research
and development of the biomedical field.
• Bioinformatics uses computational coding for
several applications that involve finding gene and
protein functions and sequences, developing
evolutionary relationships, and analyzing the three-
dimensional shapes of proteins.
• Research works based on genetic disease and
microbial disease entirely depend on bioinformatics,
 where the derived information can be vital to produce personalised
medicines.

Scope of Bioinformatics

internet
Internet is a global communication system that links together
thousands of individual networks. It allows exchange of information
between two or more computers on a network. Thus internet helps
in transfer of messages through mail, chat, video & audio conference,
etc. It has become mandatory for day-to-day activities: bills payment,
online shopping and surfing, tutoring, working, communicating with
peers, etc.
Internet was evolved in 1969, under the project called ARPANET
(Advanced Research Projects Agency Network) to connect computers
at different universities and U.S. defence. Soon after the people from
different backgrounds such as engineers, scientists, students and
researchers started using the network for exchanging information
and messages.
In 1990s the internet working of ARPANET, NSFnet and other private
networks resulted into Internet. Therefore, Internet is a global
network of computer networks’ . It comprises of millions of
computing devices that carry and transfer volumes of information
from one device to the other. Desktop computers, mainframes, GPS
units, cell phones, car alarms, video game consoles, are connected to
the Net.
How Do I Connect to the Internet?
• Computer
• Connection - Phone Line, Cable, DSL, Wireless, ...
• Modem • Network Software - TCP/IP
• Application Software - Web Browser, Email, ...
• Internet Service Provider (ISP)

What Can I Do on the Internet?

• Send and receive email messages.
• Download free software with FTP (File Transfer Protocol).
• Post our opinion to a Usenet newsgroup.
• Surf the World Wide Web.
• And much, much more.
• There is no charge for most services.

World Wide Web(WWW)

The World Wide Web (WWW) or web is an internet based service,
which uses common set of rules known as protocols, to distribute
documents across the Internet in a standard way.
World Wide Web, which is also known as a Web, is a collection of
websites or web pages stored in web servers and connected to local
computers through the internet. These websites contain text pages,
digital images, audios, videos, etc. Users can access the content of
these sites from any part of the world over the internet using their
devices such as computers, laptops, cell phones, etc. The WWW,
along with internet, enables the retrieval and display of text and
media to your device.
The World Wide Web. Or ‘Web’ is a part of the Internet. The Web is
viewed through web browser software such as Google chrome,
Internet Explorer, Mozilla Firefox etc. Using browsers one can access
the digital libraries containing innumerable articles, journals, e-
books, news, tutorials stored in the form of web pages on computers
around the world called web servers-Today thousands of web
pages/websites are added to the WWW every hour.
• The Web was invented in 1991 by Tim Berners-Lee, while consulting
at CERN (European Organization for Nuclear Research) in Switzerland.
• The Web is a distributed information system.
• The Web contains multimedia.
• Information in the Web is connected by hyperlinks. Difference
between Internet and WWW: The Internet is known as
“interconnection of computer networks”. The Internet is a massive
network of networks. It connects millions of computers together
globally, forming a network in which any computer can communicate
with any other computer as long as they are both connected to the
Internet. Information that travels over the Internet does so via a
variety of languages known as protocols. The World Wide Web, or
“Web” for short, or simply Web, is a massive collection of digital
pages to access information over the Internet. The Web uses the
HTTP protocol, to transmit data and allows applications to
communicate in order to exchange business logic. The Web also uses
browsers, such as Internet Explorer or Firefox. to access web
documents called Web pages that are linked to each other via
hyperlinks. Web documents also contain graphics, sounds, text and
video.

network basic
Network: A network is a collection of computers and devices
that are connected together to enable communication and data
exchange. Nodes: Nodes are devices that are connected to a
network. These can include computers, Servers, Printers,
Routers, Switches, and other devices.

What are the 4 types of networks?

Below mentioned are different types of networks:

• PAN (Personal Area Network)
• LAN (Local Area Network)
• MAN (Metropolitan Area Network)
• WAN (Wide Area Network)

What Is Local Area Network (LAN)?

The Local Area Network (LAN) is designed to connect multiple
network devices and systems within a limited geographical
distance. The devices are connected using multiple protocols
for properly and efficiently exchanging data and services.

Attributes of LAN Network:

• The data transmit speed in the LAN network is relatively

higher than the other network types, MAN and WAN.
• LAN uses private network addresses for network
connectivity for data and service exchange, and it uses
cable for network connection, decreasing error and
maintaining data security.
Advantages and Disadvantages of LAN Network

Advantages Disadvantages

Need constant
Transmission of data and services is
administration of
relatively higher than other network
experienced engineers
connections.
for functioning.

Probability of leak of
The Network Server acts as a central unit
sensitive data by LAN
for the whole network.
administration.

What Is a Computer Network?

A computer network is a connection between two or more network

devices, like computers, routers, and switches, to share network
resources.
The establishment of a computer network depends on the requirements
of the communication channel, i.e., the network can be wired or wireless.

Next, let’s look into the types of networks available.

Types of Networks

According to the communication requirements, multiple types of

network connections are available. The most basic type of network
classification depends on the network's geographical coverage.

Below mentioned are different types of networks:

 • PAN (Personal Area Network)

• LAN (Local Area Network)

• MAN (Metropolitan Area Network)

• WAN (Wide Area Network)

Let’s look into each of the network types in detail.

What Is Local Area Network (LAN)?

The Local Area Network (LAN) is designed to connect multiple network

devices and systems within a limited geographical distance. The devices
are connected using multiple protocols for properly and efficiently
exchanging data and services.
Attributes of LAN Network:

• The data transmit speed in the LAN network is relatively higher

than the other network types, MAN and WAN.

• LAN uses private network addresses for network connectivity

for data and service exchange, and it uses cable for network
connection, decreasing error and maintaining data security.

Advantages and Disadvantages of LAN Network

Advantages Disadvantages

Need constant
Transmission of data and services is relatively administration of
higher than other network connections. experienced engineers for
functioning.

Probability of leak of
The Network Server acts as a central unit for
sensitive data by LAN
the whole network.
administration.

What Is Wide Area Network (WAN)?

The Wide Area Network (WAN) is designed to connect devices over large
distances like states or between countries. The connection is wireless in
most cases and uses radio towers for communication.

The WAN network can be made up of multiple LAN and MAN networks.

Attributes of WAN Network:

• The speed of the WAN data transfer is lower than in comparison

to LAN and MAN networks due to the large distance covered.

• The WAN network uses a satellite medium to transmit data

between multiple locations and network towers.
Advantages and Disadvantages of WAN Network:

Advantages Disadvantages

High cost to set up the

network and the Support of
This network covers a high geographical area
experienced technicians is
and is used for large-distance connections.
needed to maintain the
network.

It is difficult to prevent
They also use radio towers and connect
hacking and debug a large
channels for users.
network.

Difference Between LAN, MAN, and WAN

Basis LAN MAN WAN

LAN is a network that Several The WAN

enables the computers network
Meaning
communication between can be extends to a
many linked devices. It is connected to much greater
in charge of establishing MAN in the area. It can
 connections among same city or link multiple
neighborhood units, separately. It countries
including universities and encompasses together.
schools. a greater
region,
including
minor towns
and cities.

MAN can be
either public
or private. A A single
LAN is a private and lot of company may
Network secured network. businesses not own
Authority Hospitals, schools, offices, and WAN. It can
etc., can own it. telephone be private or
companies public.
could own
them.

MAN
provides a WAN
The Internet speed
modest provides a
Speed provided through LAN is
Internet slow Internet
fast.
connection connection.
speed.
 MAN's
WAN
maintenance
LAN maintenance is very maintenance
Maintenance is easier
easy. is very
compared to
difficult.
LAN.

Congestion is
more in WAN
Congestion is less in the It is more in when
Congestion
LAN network. MAN. compared to
LAN and
MAN.

In MAN, WAN
The bandwidth in LAN is
Bandwidth bandwidth is bandwidth is
very high.
less. quite limited.

It isn't easy It is
It is very easy to design to design a complicated
Designing
a LAN network. MAN to design
network. WAN.

Network topology
network.[1][2] Network topology can be used to define or describe the
arrangement of various types of telecommunication networks,
including command and control radio
networks,[3] industrial fieldbusses and computer networks Network
topology is the arrangement of the elements (links, nodes, etc.) of a
communication

Diagram of different network topologies.

What are network protocols

Network protocols are a set of rules outlining how connected devices
communicate across a network to exchange information easily and
safely. Protocols serve as a common language for devices to enable
communication irrespective of differences in software, hardware, or
internal processes.

Types
• Transmission Control Protocol (TCP) A.K.A. Internet Protocol (IP)
• User Datagram Protocol (UDP)
• File Transfer Protocol (FTP)
• Hypertext Transfer Protocol (HTTP)
• Simple Network Management Protocol (SNMP)
• Internet Control Message Protocol (ICMP)
• Post Office Protocol (POP)

There are three main types of network protocols you need to be aware of:
 • Network management protocols – These protocols set out
policies designed to monitor, manage and maintain a network.
Examples include SNMP, FTP, POP3 and Telnet.
• Network communication protocols – A group of protocols
used to establish rules and formatting (such as syntax,
synchronization and semantics) for exchanging data across a
network. Types of network communication protocols include TCP,
UDP, IP, HTTP, IRC, BGP and ARP.
• Network security protocols – Security protocols are protocols
that use security measures such as cryptography and encryption to
protect data. Examples include SFTP, SSL and HTTPS.
3. File Transfer Protocol (FTP)

FTP is a network protocol that’s used to transfer files from one device to
another over an unencrypted TCP/IP connection. With FTP, a user can
load up a web browser or FTP client such as FileZilla or FTP Voyager and
send up to 2GB at once.

Many organizations use FTP because of its ability to send large files or
lots of files at once in a way that’s fast and efficient. Unfortunately, this
efficiency comes at the cost of security as FTP transmits all data in plain
text.

For this reason, many organizations opt to use a secure version of FTP
called File Transfer Protocol Secure Sockets Layer (FTPS), which
functions the same but uses SSL encryption to obscure the transferred
data.

4. Hypertext Transfer Protocol (HTTP)

HTTP is a communication protocol that enables systems to communicate

on the World Wide Web. With HTTP, a client will send a hypertext
message request to a web server asking for access to the resources
needed to load a web page.

The server hosting the content will then respond and enable the client to
load all the necessary text, images and videos featured on the page.
HTTP’s request-response cycle is outlined briefly below:

• The client sends an HTTP request message to the web server to

request access to the web page content.
 • The web server processes the request message.
• The web server sends a response message that includes the
requested content or web page.
• The client receives the message and loads the content in the web
browser for the end user to view.
There is also an encrypted version of HTTP called HTTPS, which uses
SSL/TLS encryption to encrypt requests and responses so they can’t be
accessed by third parties.

Division of Bioinformatics

Recently, it has become possible to analyze massive amounts of human

genome data, including the entire human genome sequence,
comprehensive gene expression and microRNA (miRNA) that regulates
the gene expression. Our aim is to identify disease biomarkers and
develop innovative diagnostic and therapeutic methods via these large-
scale human genome data.
What are the major challenge in bioinformatics
Some major challenges in bioinformatics include:

1. Handling and analyzing large and complex data sets, such as

genome sequences and gene expression data.
2. Developing accurate and efficient algorithms for various
bioinformatics tasks, such as sequence alignment, gene
prediction, and phylogenetic reconstruction.
3. Integrating and making sense of data from different sources and
levels of information, such as genetic, epigenetic, transcriptomic,
and proteomic data.
4. Addressing the ethical and legal issues related to the storage,
sharing, and use of genomic data.
5. Keeping up with the rapid pace of technological advancements in
areas such as DNA sequencing and data storage.
6. Improving the reproducibility and transparency of bioinformatics
research.
7. Addressing the scalability challenges in bioinformatics especially
when dealing with large data sets.
8. Developing user-friendly and accessible tools for bioinformatics
analysis and data management.