Cover Page

Basic Applied Bioinformatics


Chandra Sekhar Mukhopadhyay

Ratan Kumar Choudhary

Mir Asif Iquebal


With contributions from


Ravi GVPPS Kumar, Sarika, Dinesh Kumar, Aditya Prasad Sahoo, Amit Kumar, Saurabh Jain, Surbhi Panwar, Ashwani Kumar, Harpreet Kaur Manku










Dedicated to students, researchers and professionals


Bioinformatics, a discipline that attempts to make predictions about biological functions using data from molecular sequence (nucleotide and protein) analysis and involves application of information science to biology has, over the years, evolved exponentially in the genomics era. Today it has become an indispensable component of biological science, including its application in a number of applied areas.

There has long been a need among students and researchers for a primer book on the application of bioinformatics tools in various spheres of veterinary and agricultural sciences. This being the era of multi‐tasking, research workers who do not possess a background in computer or bioinformatics often stumble over in silico analysis of molecular data. This book provides practical know‐how for graduate students of bioinformatics, biotechnology and other streams of biological science, and also for those who need to learn bio‐computational analyses of the large volume of molecular data that is being generated in thousands of laboratories throughout the world.

The topics considered in this book are the basic ones that a student or researcher of the fields above should know. In addition, this book covers the syllabi of the graduate or undergraduate course called “Introduction to Bioinformatics” (or course name similar to that) that is offered in several universities. Some of the chapters, covering areas such as genome annotation in prokaryotes and eukaryotes, an overview of microarray data analysis, use of MISA for microsatellite sequence identification and SNP mining, have also been introduced for out‐of‐the‐box applications.

In general, the book serves as a reference book for those working in biocomputational research and studies. The contents of this book cover wider areas of bioinformatics. Several freely available software tools (online or offline) are available, and students and researchers can use them for in silico analysis. However, in some instances, students become stuck while optimizing parameters for data analysis and drawing appropriate inferences. Also, they are often not familiar with several terminologies. This book explains steps for parameter optimization of the tools being used, as well as the basic terminologies. The results obtained have been explained, to demonstrate how inferences are drawn.

This book can also serve as a practical manual for the elucidation of critical steps, with annotation and explanation. It begins with basic aspects of bioinformatics, including frequently used terminology, concept development, handling molecular sequences, BLAST analyses, primer designing, phylogenetic tree construction, prediction of protein structures and genome annotation. In the last few chapters, some advanced topics of bioinformatics have been covered, such as analysis of transcriptome data, identification of differentially expressed genes and prediction of microRNA targets.

Each chapter demonstrates the steps with an example, which involves stepwise elucidation of the procedures and explanation of the obtained results. The practical methodology is depicted with screenshots of the software being used, along with legends to explain the screenshot view. New terminologies introduced in some chapters have been provided. Additionally, four or five questions are given at the end of each chapter, with any hints which are deemed to be required for some questions.

We believe that there could be some unintentional mistakes remaining in this book. We sincerely request the reader to apprise the editors for typographical or other errors, if found. It is very common that the version of molecular sequences in public repository is updated over time, or sometimes one or more sequence entries are deleted. The readers are requested to update the editors about such changes. Similarly, the uniform resource locators (URLs) of the websites containing bioinformatics tools or databases can change suddenly. We will be careful to update these changes in the next edition of the book. Readers are also requested to assist us in this regard.

It is hoped that this book will be a useful primer for beginners of this fast‐expanding field.


We thank Ms. Mindy Okura‐Marszycki and Mr. Vishnu Narayanan of Wiley for their timely help and encouragements. We extend a special note of thanks to Prof. G.S. Brah, Founder Director, and Prof. Ramneek Verma, Director, of the School of Animal Biotechnology, GADVASU, Ludhiana, for providing the conducive working environment and for inspiring us to contribute to the field of bioinformatics. They evaluated some of the chapters and raised critical questions for improving the quality. The authors thankfully appreciate Miss J.K. Dhanoa and Ms. H.K. Manku for thoroughly checking the syntax of the manuscript, helping in editing and framing the diagrams in the proper format. The chapters were also evaluated for lucidness and ease of understanding by the graduate students of the Iowa State University, Mrs. Supreet Kaur (MSc Biochemistry) and Shravanti Krishna (PhD Biochemistry). Sincere thanks are extended to Dr. Nikhlesh Singh (Assistant Professor, Physiology, the University of Tennessee Health Science Center (UTHSC), Memphis, USA), Dr Monson Melissa (Postdoc Research Associate, Animal Science, Iowa State University) and Dr. Sangita Singh (Post Doc., Department of Food Science and Human Nutrition, Iowa State University) for their constructive criticisms to improve the chapters. Dr. Shivani Sood, Assistant Prof. (Biotechnology, Mukand Lal National College, Yamuna Nagar, Haryana, India), deserves special mention for critically checking the chapters and giving constructive input. All the freely available software and databases covered in this book are duly acknowledged. We are obliged to all those who have directly or indirectly contributed to writing this book.

Our sources of inspiration have been our families, colleagues and students. Nevertheless, we bow before the Almighty and Mother Nature for giving us the potential to accomplish the task.