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Introduction To Bioinformatics

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Jagmohan Rana Dr. Kunwar Singh Vaisla

Hemwati Nandan Bahuguna Garhwal University Bipin Tripathi Kumaon Institute of Technology Dwarahat INDIA
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1
 BIOINFORMATICS
Tools & Applications

Editor-in-Chief
Dr. J.M.S Rana, Ph.D.
Director,
Uttarakhand State Biotechnology Department,
Government of Uttarakhand

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Uttarakhand State Biotechnology Department

(Ministry of Science & Technology and Biotechnology)
Government of Uttarakhand

2012
Edi t or :
Dr. Kunwar Singh Vaisla, Ph.D.
Associate Professor,
Department of Computer Science & Engineering
BT Kumaon Institute of Technology
Dwarahat 263653, District Almora (Uttarakhand)
[email protected]

Co-Edi t or :
Mr. Rajendra Bharti,
Associate Professor,
Department of Computer Science & Engineering
BT Kumaon Institute of Technology
Dwarahat 263653, District Almora (Uttarakhand)

BIOINFORMATICS - Tools & Applications

ISBN: 978-81-923296-3-5
© copyright 2012, Rana
All rights are reserved. Utilization of this publication, other than stated, is prohibited
without prior written permission of the editor-in-chief.

Disclaimer :
This document may be freely reviewed, abstracted, reproduced and translated in part
or in whole, but not for sale of any commercial purpose. All reasonable precautions
have been taken by editorial board and authors to verify the information contained in
this publication. However, the responsibility for the interpretation of the material and
warranty of any kind, either expressed or implied, lies with the reader.

The document is being published by USBD for free of cost distribution among
trainees/participants/students.

A Joi nt Publ i cat i on of :

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Uttarakhand State Biotechnology Department(Ministry of Science &

Technology and Biotechnology), Government of Uttarakhand.

And

Department of Computer Science & Engineering

BT Kumaon Institute of Technology
Dwarahat 263653, District Almora (Uttarakhand)

Printed by:
Charu Printers, Dehradun
Phone : 0135-2727591
(Dr. C. Raman Suri)
Chief Scientist
Head-Nanobiotechnology
 PREFACE
The unprecedented growth of computer science and
biotechnology has rapidly spawned specialized research groups and
industries, both. Bioinformatics, generally relates to biological
molecules and therefore requires knowledge and understanding in the
field of biochemistry, molecular biology, biophysics, mathematical
modeling, to name a few. Thus, Bioinformatics is a multi-disciplinary
field with an appropriate convergence of computer science, information
technology, biotechnology etc. encompassing analysis and
interpretation of biological data, modeling of biological processes and
development of related algorithms and statistics. Bioinformatics aims to
solve some of the important biological problems using computational
techniques and applications. Prominent among such examples include
those to gene-protein interactions, various protein structure prediction,
molecular networks, structures and sequences, and genomics and
proteomics. The knowledge of bioinformatics helps us tremendously in
analysis and interpretation of various types of biological data including
nucleotide and amino-acid sequences, protein domains /folding and
protein structures etc. It is the knowledge of bioinformatics which made
it possible to discover all human genes (per human genome
approximately 3 billion base pairs) determine complete sequence of 3
billon DNA subunits and make them accessible for further biological
studies. Thus, the research in this field requires close collaboration
among multi-disciplinary teams of researchers in computer science,
statistics, physics, engineering, life sciences medical sciences, and their
interfaces.

This compendium “Bioinformatics: Tools and Applications”

comprises of 12 articles chiefly introductory in nature, however with
insight to some important research challenges. The articles have been
selected on the basis of their fundamentality rather than the
rigorousness /thoroughness of techniques deployed. The compendium
represent the output of the lectures delivered in the Uttarakhand State
Biotechnology Department (USBD), sponsored short term training
program “Bioinformatics tools and its applications” Organized at B.T.
Kumaon Institute of Technology, Dwarhat(Almora) during 16 28 July
2012.

We are indebted to Hon'ble Chief Minister/ Chairman

Uttarakhand Biotechnology Board and Hon'ble Minister (Science &
Technology and Biotechnology) /vice Chairman Uttarakhand
Biotechnology Board, Govt. of Uttarakhand for their interest, care and
blessings for overall development of Biotechnology in the State. We also
extend our sincere thanks to Secretary and additional Secretary,
Ministry of Science & Technology and Biotechnology, Govt. of
Uttarakhand for their valuable guidance and support.

We are highly thankful to all the learned resource persons of the

training program for their great work and interest to provide the articles
for this compendium. I would like to place on record my sincere
gratitude and obligations to Mr Surendra Singh Negi, Honb'le Cabinet
Minister, Science & Technology and Biotechnology, Government of
Uttarakhand for sending us his valuable Message for the Compendium.
I need to express my heartfelt thanks, indeed gratefulness, to Dr C.
Raman Suri, Chief Scientist & Head Nanobiotechnology Division, CSIR
- Institute of Microbial Technology, Chandigarh for his unflinching
cooperation and for very kindly writing the Foreword of this
compendium. We are highly obliged and grateful to Reviewers of this
compendium for critically reviewing the manuscript.

Finally I wish to express my Special thanks to Dr. Kunwar Singh

Vaisla and Dr Rajendra Kumar Bharati, BT Kumaun Institute of
Technology, Dwarhat(Almora) for their competent and comprehensive
editorial task. The views expressed in the compendium are solemnly
those of the authors. Despite the careful efforts in compilation of the
compendium, remaining errors may kindly be pardoned and brought to
the notice for further improvement.

We hope the book will be useful to students and academicians

working in the field of Bioinformatics, Biotechnology, and other related
fields of studies.

(J.M.S.Rana)
 INDEX

Ch Topic Page No
No.
1 Message 3
2 Forward 5
3 Preface 7
4 Introduction To Bioinformatics 11
Jag Mohan Singh Rana & Kunwar Singh Vaisla

5 Introduction Of Molecular Biology 19

T. Kalaivani & C. Rajasekaran

6 Nucleic Acid And Protein Sequences 28

I. Arnold Emerson & C. Immanuel Selvaraj
Biological And Bioinformatics 34
7 Databases And Data Mining
A. K. Mishra

8 Mathematical Modeling & Simulation 58

Sanjay Kumar Agarwal
Sequence Analysis And Computational 68
9 Models For Biological Data
C. Immanuel Selvaraj & I. Arnold Emerson

10 Phylogenetic Analysis 74
Kumar Sachin

11 Sequence Analysis Languages And Tools 94

C. K. Jain

12 Proteomics 113
C. Rajasekaran & T. Kalaivani

13 DNA Representation 134

Ms. Archana Verma

14 Biological Sequence Compression 143

Mr. Rajendra Bharti

15 Bioinformatics Tools 158

Kunwar Singh Vaisla & Jag M ohan Singh Rana
16 About Authors 176
 Introduction to Bioinformatics
Jag Mohan Singh Rana & Kunwar Singh Vaisla

What is Bioinformatics ?
Bioinformatics is an interdisciplinary research area at the interface
between biological and computational sciences. Although the term
'Bioinformatics' is not really well-defined, you could say that this
scientific field deals with the computational management of all kinds of
molecular biological information. Most of the bioinformatics work that
is being done deals with either analyzing biological data, or with the
organization of biological information.
As a consequence of the large amount of data produced in the field of
molecular biology, most of the current bioinformatics projects deal with
structural and functional aspects of genes and proteins.
Defining the terms bioinformatics and computational biology is not
necessarily an easy task, as evidenced by multiple definitions available
over the web. A recent google search for "definition of bioinformatics"
returned over 43,000 results! In the past few years, as the areas have
grown, a greater confusion into these two terms has prevailed. For
some, the terms bioinformatics and computational biology have become
completely interchangeable terms, while for others, there is a great
distinction. I'll throw my two cents in, based on what my experience has
been to the consensus use of these two terms.
Computational biology and bioinformatics are multidisciplinary fields,
involving researchers from different areas of specialty, including (but in
no means limited to) statistics, computer science, physics,
biochemistry, genetics, molecular biology and mathematics. The goal of
these two fields is as follows:
• Bioinformatics: Typically refers to the field concerned with the
collection and storage of biological information. All matters
concerned with biological databases are considered
bioinformatics.
• Comput at ional
biology: Refers to the
aspect of developing
algorithms and
statistical models
necessary to analyze
biological data through
the aid of computers.

Image Source: http://ccb.wustl.edu/

Bioinformatics Tools & Its Applications 11

Understanding of bioinformatics and computational biology follows the
NIH definitions listed below:
• Bioinformatics: Research, development, or application of
computational tools and approaches for expanding the use of
biological, medical, behavioral or health data, including those to
acquire, store, organize, archive, analyze, or visualize such data.
• Computational Biology: The development and application of
data-analytical and theoretical methods, mathematical
modeling and computational simulation techniques to the study
of biological, behavioral, and social systems.

Others have offered various opinions into these definitions as well:

http://kbrin.kwing.louisville.edu/~rouchka/definition.html
So why is bioinformatics a hot field? One answer to this question is that
it is tied to the human genome project which has generated a lot of
popular interest. Various advances in molecular biology techniques
(such as genome sequencing and microarrays) has led to a large amount
of data that needs to be analyzed. Now that we are close to having the
human genome finished, what does it all mean? That's where
bioinformatics steps in. Bioinformatics can lead to important
discoveries as well as help companies save time and money in the long
run. In addition, there needs to be methods to manage large amounts of
data. One of the biggest reasons for bioinformatics being a hot field is
the old supply and demand adage. There just are too few people
adequately trained in both biology and computer science to solve the
problems that biologists need to have solved.
1. Emergence of Bioinformatics
Biological data are flooding in at an unprecedented rate. For example as

12 Bioinformatics Tools & Its Applications

of August 2000, the GenBank repository of nucleic acid sequences
contained 8,214,000 entries and the SWISS-PROT database of protein
sequences contained 88,166. On average, the amount of information
stored in these databases is doubling every 15 months. In addition,
since the publication of the H. influenzae genome, complete sequences
for over 40 organisms have been released, ranging from 450 genes to
over 100,000. Add to this the data from the myriad of related projects
that study gene expression, determine the protein structures encoded
by the genes, and detail how these products interact with one another,
and we can begin to imagine the enormous quantity and variety of
information that is being produced.
Thus there are three important factors that facilitated the emergence of
Bioinformatics during the early 1960s which are as following:
1. First, an expanding collection of amino-acid sequences provided
both a consource of data and a set of interesting problems that
were infeasible to solve without the number-crunching power of
computers.
2. Second, the idea that macromolecules carry information became
a central part of the conceptual framework of molecular biology.
Although some historians and philosophers have questioned the
theoretical significance of this idea for modern molecular
biology57, it seems likely that thinking in terms of
macromolecular information provided an important conceptual
link between molecular biology and the computer science from
which formal information theory had arisen.

Fig 1: Growth of Biological data in various databases

(Source: http://www.genome.jp/en/db_growth.html)
3. Third, high-speed digital computers, which had developed from
weapons research programmes during the Second World War,
finally became widely available to academic biologists. Not all
biologists had or wanted to have access to these machines but,
by 1960, scarcity of computers was no longer a serious
stumbling block for the development of computational biology.

Bioinformatics Tools & Its Applications 13

 Fig 2: Basic Components of Bioinformatics

2. Aims of bioinformatics
The aims of bioinformatics are three-fold.
1. First, at its simplest bioinformatics organises data in a way that
allows researchers to access existing information and to submit
new entries as they are produced, e.g. the Protein Data Bank for
3D macromolecular structures .
2. While data-curation is an essential task, the information stored
in these databases is essentially useless until analysed. Thus the
purpose of second aim is to develop tools and resources that aid
in the analysis of data.
3. The third aim is to use these tools to analyze the data and
interpret the results in a biologically meaningful manner.
Traditionally, biological studies examined individual systems in detail,
and frequently compare them with a few that are related. In
bioinformatics global analyses of all the available data with the aim of
uncovering common principles that apply across many systems and
highlight features that are unique to some.
Research Areas of Bioinformatics

14 Bioinformatics Tools & Its Applications

Current research in bioinformatics can be classified into:
(i) Genomics :- Genomics is the study of an organism's genome.
This term is given by Thomas H. Roderick in 1987.

Fig 4: Areas of Genomics

(ii) Proteomics :- It is defined as the study of the proteome.

Proteome refers to the entire set of expressed proteins in a cell.

Fig 5: Areas of Proteomics

(iii) Computer Aided Drug Designing : Computer-Aided Drug

Design (CADD) is a specialized discipline that uses
computational methods to simulate drug-receptor interactions.
CADD methods are heavily dependent on bioinformatics tools,
applications and databases.

Fig 6: Study of Interaction of a drug in biological environment

(Source: http://www.mpi-inf.mpg.de/
departments/d3/areas/docking.html )
(iv) Biological database: Biological databases are libraries of life
sciences information, collected from scientific experiments,
published literature, high-throughput experiment technology,
and computational analyses. They contain information from
research areas including genomics, proteomics, metabolomics,
microarray gene expression, and phylogenetics. Information
contained in biological databases includes gene function,
structure, localization (both cellular and chromosomal), clinical
effects of mutations as well as similarities of biological sequences
and structures.

Bioinformatics Tools & Its Applications 15

 Fig 7: Types of Biological Databases

(Source: http://www.mrc-lmb.cam.ac.uk/genomes/
madanm/pres/biodb.htm )
(v) Biological Data Mining: Biological Data mining is the discovery
of useful knowledge from biological databases. Data mining
employs algorithms and techniques from statistics, machine
learning, artificial intelligence, databases and data warehousing
etc. Some of the most popular tasks are classification,
clustering, association and sequence analysis, and regression.
Clustering, association and sequence analysis, and regression.

Fig 8: Various steps involved in Data Mining

(Source: http://cs.salemstate.edu/hatfield/
teaching/courses/DataMining/M.htm )
(vi) Microarray informatics: Microarray Technology is a powerful
tool to monitor gene expression or gene expression changes of
hundreds or thousands of genes in a single experiment.

Fig 9: Principle of Microarray Analysis for gene Expression

(Source: http://www.accessexcellence.org/RC/
VL/GG/microArray.php )
16 Bioinformatics Tools & Its Applications
(vii) Molecular Phylogenetics: Molecular phylogenetics is the study of
organisms on a molecular level to gather information about the
phylogenetic relationships between different organisms.

Fig 9: Phylogenetic relation between various organisms

(Source: http://www.tulane.edu/~wiser/
protozoology/notes/tree.html )

(viii) System biology: Systems biology studies biological systems by

systematically perturbing them (biologically, genetically, or
chemically); monitoring the gene, protein, and informational
pathway responses; integrating these data; and ultimately,
formulating mathematical models that describe the structure of
the system and its response to individual perturbations.

Bioinformatics Tools & Its Applications 17

 Fig 10: Modeling and System Biology

(Source: http://kdbio.inesc-id.pt/~orlando/kdbio/software.html)

(ix) Agro-informatics: Agricultural informatics concentrates on the

aspects of Bioinformatics dealing with plant genomes. The term
“Agri-Informatics” (AI) is coined to cover broadly for all types of
development and applications of computerized information
technology-based solutions for gathering, managing and
analyzing data produced by agricultural systems and to develop
models and forecasting systems.
Reference
1. Introduction to Bioinformatics T.K. Attwood and Parry Smith
2. Introduction to Bioinformatics Arthur M. Lesk
3. Fundamental Concepts in Bioinformatics Krane and Raymer
4. http://kbrin.kwing.louisville.edu/~rouchka/definition.html

18 Bioinformatics Tools & Its Applications

 ABOUT AUTHORS

S. Author Name Author Designation and Affiliation

No.
Director,
1 Dr. Jag Mohan Singh Rana Uttarakhand State Biotechnology Department,
Government of Uttarakhand, Dehradun
Associate Professor,
Department of Computer Science & Engineering,
2 Dr. Kunwar Singh Vaisla
BT Kumaon Institute of Technology,
Dwarahat – 263653, District – Almora, Uttarakhand
Associate Professor,
3 Dr. T. Kalaivani School of Bio Sciences and Technology
VIT University, Vellore – 632014 Tamilnadu
Associate Professor,
4 Dr. C. Rajasekaran School of Bio Sciences and Technology
VIT University, Vellore – 632014 Tamilnadu
Associate Professor,
5 Dr. I. Arnold Emerson School of Bio Sciences and Technology
VIT University, Vellore – 632014 Tamilnadu
Associate Professor,
6 Dr. C. Immanuel Selvaraj School of Bio Sciences and Technology
VIT University, Vellore – 632014 Tamilnadu
Sr. Scientist,
7 Dr. A. K. Mishra
Bioinformatics Center, USI, IARI, New Delhi-12
Associate Professor,
8 Dr. Sanjay Kumar Agarwal Department of Stat-Math,
Dolphin PG Institute,Manduwala, Dehradun
Associate Professor,
9 Dr. Kumar Sachin Sri Bhagwan Singh Post Graduate Institute,
Balawala, Dehradun
Professor
10 Dr. Chakresh Kumar Jain Jaypee Institute Information Technology
Noida
Assistant Professor
Department of Computer Science & Engineering
11 Ms. Archana Verma
BT Kumaon Institute of Technology
Dwarahat – 263653, District – Almora (Uttarakhand)
Assistant Professor
Department of Computer Science & Engineering
12 Mr. Rajendra Bharti
BT Kumaon Institute of Technology
Dwarahat – 263653, District – Almora (Uttarakhand)

176 Bioinformatics Tools & Its Applications

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