Bioinformatics : A Practical Guide to NCBI Databases and Sequence Alignments book cover
1st Edition

A Practical Guide to NCBI Databases and Sequence Alignments

ISBN 9781032123691
Published March 23, 2022 by Chapman and Hall/CRC
468 Pages 398 Color & 23 B/W Illustrations

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Book Description

Bioinformatics: A Practical Guide to NCBI Databases and Sequence Alignments provides the basics of bioinformatics and in-depth coverage of NCBI databases, sequence alignment, and NCBI Sequence Local Alignment Search Tool (BLAST). As bioinformatics has become essential for life sciences, the book has been written specifically to address the need of a large audience including undergraduates, graduates, researchers, healthcare professionals, and bioinformatics professors who need to use the NCBI databases, retrieve data from them, and use BLAST to find evolutionarily related sequences, sequence annotation, construction of phylogenetic tree, and the conservative domain of a protein, to name just a few. Technical details of alignment algorithms are explained with a minimum use of mathematical formulas and with graphical illustrations.

Key Features

  • Provides readers with the most-used bioinformatics knowledge of bioinformatics databases and alignments including both theory and application via illustrations and worked examples.
  • Discusses the use of Windows Command Prompt, Linux shell, R, and Python for both Entrez databases and BLAST.
  • The companion website ( contains tutorials, R and Python codes, instructor materials including slides, exercises, and problems for students.

This is the ideal textbook for bioinformatics courses taken by students of life sciences and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.

Table of Contents


Preface, vii

Acknowledgments, ix

Chapter 1 | The Origin of Genomic Information 1

Chapter 2 | The Sources of Genomic Data 39

Chapter 3 | The NCBI Entrez Databases 77

Chapter 4 | NCBI Entrez E- Utilities and Applications 265

Chapter 5 | The Entrez Direct 289

Chapter 6 | R and Python Packages for the NCBI E- Utilities 343

Chapter 7 | Pairwise Sequence Alignment 383

Chapter 8 | Basic Local Alignment Search Tool 407

INDEX, 453

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Hamid D. Ismail earned his Ph.D. and M.Sc. in computational science from North Carolina Agricultural and Technical State University, USA, and Doctor of Veterinary Medicine (DVM) and Applied Diploma in Statistics and Programming from the University of Khartoum, Sudan. He has worked as an adjunct professor, bioinformatics specialist, bioinformatics tool developer, senior scientist, statistician, and database consultant with several institutions. He is currently a Ph.D. Research Associate at North Carolina Agricultural and Technical State University. Dr. Ismail is a published author in bioinformatics, statistics, machine learning, and bio-science, and hehas developed a number of bioinformatics desktop and web-based applications. He is also a reviewer for a number of academic journals.


Bioinformatics is a necessary text that will help researchers/students gain background knowledge and understand the usage of NCBI databases. It is well suited for audiences who do not have a bioinformatics background as it defines what genomic data is and the fundamentals of the sequence alignment. It also thoroughly explains how to use NCBI tools to retrieve the researchers' genomic data of interest.

-- Roshonda Jones, Senior Bioinformatics Scientist, Nom Nom