Computational Genomics and Structural Bioinformatics in Microbial Science

Microbial Genomics Volume 2

1st Edition - February 24, 2025
Imprint: Academic Press
Editors: Javid Ahmad Parray, Niraj Singh, Wen-Jun Li
Language: English
Paperback ISBN:
9 7 8 - 0 - 4 4 3 - 3 1 5 5 0 - 3
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 3 1 5 5 1 - 0

Computational Genomics and Structural Bioinformatics in Microbial Science: Microbial Genomics (Volume 2) covers different aspects of microbial genomics, metagenomics, and functi… Read more

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Computational Genomics and Structural Bioinformatics in Microbial Science: Microbial Genomics (Volume 2) covers different aspects of microbial genomics, metagenomics, and functional studies of microbes through informative illustrations of current trends in computational tools and bioinformatics approach in environmental microbiology and clinical diagnosis. This book aims to provide readers with an overview of the microbial genome, computational genomics, and structural bioinformatics in microbial science, as well as the most recent developments in these fields. This book covers a range of topics, including the challenges and opportunities of computational epigenomics, bioinformatics tools for assessing metagenomic data, as well as computed comparative genomics and computational phenotyping of microorganisms relevant to agriculture. Microbial Genomics: Host Adaptation, virulence, and Evolution is a valuable resource for faculty members, researchers, and undergraduate and postgraduate students at universities, medical research labs, that are interested in microbial science specifically related to the microbial genome, computing genomics, and bioinformatics.

Title of Book
Cover image
Title page
Table of Contents
Copyright
List of contributors
Preface
Acknowledgment
Section I: Introduction to bioinformatics and metagenomics
Chapter 1. Introduction to bioinformatics in microbial biotechnology
Abstract
1.1 Introduction
1.2 Sequencing of genomes
1.3 Rebuilding metabolic chain
1.4 Reexamining microbial evolution
1.5 Bioinformatics applications
1.6 Conclusion
References
Chapter 2. Analysing microbial proteins: bioinformatic approaches for molecular structure and function characterization
Abstract
2.1 Introduction
2.2 A brief overview of genome sequencing
2.3 An overview of protein sequence, structure and structure databases
2.4 Platforms to construct novel and reliable protein structural models
2.5 Protein structural model visualization softwares
2.6 Docking of three-dimensional protein structures
2.7 Molecular dynamics simulation of proteins
2.8 Conclusion
Acknowledgement
References
Chapter 3. Microbial mosaics: understanding ecosystems through short read metagenomics
Abstract
3.1 Introduction
3.2 Short-read sequencing techniques for microbial metagenome next-generation sequencing
3.3 Quality assessment of metagenome next-generation sequencing short-read data
3.4 Removal of short reads from host genome
3.5 Taxonomic concordance and correlation coefficient analysis of short reads
3.6 Metagenome assembly and binning
3.7 Assessment of assembled metagenome and its quality
3.8 Annotation of assembled metagenome
3.9 Conclusion
References
Chapter 4. Sequencing the unseen: long-read metagenomics and the microbial frontier
Abstract
4.1 Discovery of new microorganisms: premetagenomics era
4.2 Shift paradigm from culture-dependent methods to culture-independent ones: paving the way to advanced microbiome analysis
4.3 Metagenomics: emerging a novel concept to discover the unseen microorganisms
4.4 DNA sequencing technology: from basic technology to advanced analysis
4.5 Next-generation sequencing
4.6 Conclusion
Abbreviations
References
Chapter 5. Navigating the frontier: computational approaches in antimicrobial drug discovery
Abstract
5.1 Introduction
5.2 Computational approaches in antimicrobial drug discovery
5.3 Current challenges of computer-aided antimicrobial drug discovery
5.4 Conclusion
Conflict of interest
References
Section II: Computational genomics and epigenomics - challenges and opportunities
Chapter 6. Computational genomics: finding out mystery of whole genome
Abstract
6.1 GGCAT and de Bruijin graphs
6.2 Gene regulatory networks
6.3 Third-generation sequencing
6.4 Chhoti Anhoni and Badi Anhoni
6.5 Genome analysis of West Nile virus
References
Chapter 7. Computational epigenomics: challenges and opportunity
Abstract
7.1 Introduction
7.2 Analyzing and processing epigenetic data
7.3 Types of samples and methods for processing samples
7.4 Data handling and workflows
7.5 Coordinated pipelines
7.6 Data interpretation and functional analysis
7.7 Gene ontology
7.8 Pathway analysis
7.9 Interactomes
7.10 Integrated frameworks
7.11 Computational epigenomics databases
7.12 Next-generation sequencing and epigenomics
7.13 Applications of computational epigenomics
7.14 Prospects and current research area
7.15 Conclusion
References
Chapter 8. Decoding the blueprint: an overview of genome sequencing, assembly, and annotation
Abstract
8.1 Introduction
8.2 Preprocessing of whole genome sequencing data
8.3 Genome assembly
8.4 Polishing of genome assembly
8.5 Assessment of assembled genome
8.6 Annotation of assembled genome
8.7 Conclusion
References
Chapter 9. Computational approaches to unraveling microbial genomic diversity
Abstract
9.1 Introduction
9.2 Genome assembly
9.3 Gene prediction and annotation
9.4 Metagenomics
9.5 Functional genomics
9.6 Systems biology approaches
9.7 Future directions and conclusion
9.8 Conclusion
References
Chapter 10. Computational tools and databases of microbes and its bioprospecting for sustainable development
Abstract
10.1 Introduction
10.2 Role of bioinformatics and databases in bioprospecting
10.3 Tools and databases
10.4 Conclusion and future prospect
References
Chapter 11. Computational biology methods and their application to comparative genomics
Abstract
11.1 Introduction
11.2 Conclusion
AI disclosure
References
Section III: Structural bioinformatics
Chapter 12. Structural bioinformatics
Abstract
12.1 Introduction
12.2 Structural study of proteins
12.3 How protein structures are formed?
12.4 Importance of protein folding
12.5 Data banks
12.6 Molecular visualization
12.7 Protein–protein interaction
12.8 Importance of protein–protein interaction
12.9 Molecular docking
12.10 Conclusion
Conflict of interest
Source of funding
References
Chapter 13. Bridging genomes and structures: the mechanistic role of structural bioinformatics in genomic genetic variation
Abstract
13.1 Introduction
13.2 Structural bioinformatics: a key player
13.3 Role in deciphering the impact of genetic variations
13.4 Structural modeling techniques
13.5 Challenges and limitations in structural biology
13.6 Conclusion
References
Chapter 14. Molecular structure and role of microbial proteins: a delimitation employing bioinformatics techniques
Abstract
14.1 Introduction
14.2 Fundamentals of protein sequence to structural form
14.3 Microbial protein sequence and structure-based bioinformatics software and tools
14.4 Structure-based approach
14.5 Artificial intelligence in protein understanding
14.6 Utilization of bioinformatics in the realm of protein engineering
14.7 Conclusion
Abbreviations
References
Chapter 15. Genomic characterization and computational phenotyping of agriculturally important microbes
Abstract
15.1 Introduction
15.2 Genomic characterization of microbes associated with agriculture
15.3 Characterization of plant growth-promoting bacteria
15.4 Characterization of plant growth-promoting bacteria with antagonistic ability
15.5 Characterization of plant growth-promoting bacteria with stress tolerance
15.6 Characterization of pathogenic bacteria
15.7 Computational phenotyping of microbes associated with agriculture
15.8 Conclusion
References
Chapter 16. Revolutionizing metagenomic screening with computational algorithms
Abstract
16.1 Introduction
16.2 Metagenomics and screening approaches
16.3 Compiling metagenomic reads
16.4 Classifying metagenomic reads to assign taxonomic labels
16.5 Predicting metabolite patterns using metagenomic data
16.6 Future perspectives
References
Index

Javid Ahmad Parray

Javid A Parray is currently teaching at the Department of Environmental Science, GDC Eidgah, affiliated to Cluster University, Srinagar. His research interests include ecological and agricultural microbiology, climate change, microbial biotechnology, and environmental microbiomes. He has also done his Post Doctorate Research from the University of Kashmir. Dr Parray was also awarded a Fast Track Young Scientist Project by SERB – DST, GoI New Delhi. Dr Javid was also awarded as “Emerging scientist year Gold Medal” for the year 2018 by Indian Academy of Environmental Science. Dr Parray is the course coordinator for the UG- Programmes for CeC-MOOCS Swayam in Environmental Science. Dr Parray is an expert review member in the field of environmental science in the CSTT, Ministry of Education, GoI New Delhi.

Affiliations and expertise

Assistant Professor and Head of the Department of Environmental Science, Govt. SAM Degree College - Budgam, India

Niraj Singh

Dr Niraj Singh holds a master's degree in Molecular Biology and Biotechnology and completed his PhD in Molecular Microbiology from the Department of M.B.B.T, Tezpur University, Assam India. After completing his Ph.D. Degree, Dr. Niraj Singh started his teaching career at the Department of Botany, North Eastern Hill University, Shillong, Meghalaya. India. He currently works at the Department of Microbiology, The Assam Royal Global University, Guwahati, Assam as an Assistant Professor & Coordinator/Head. His current area of research is R. solanacearum bacterial wilt disease in plants, Virulence gene function study of R. solanacearum, and its control in agronomically important crops. He has published quality research articles and book chapters. Dr. Niraj Singh was also awarded the Hayward-Prior Travel Award 2020 for Ralstonia solanacearum wilt research work, the Young Scientist Award, the Young Plant Pathologist Award, and the certificate of appreciation at Gujrat Vigyan Sammelan in 2022.

Affiliations and expertise

Department of Microbiology, The Assam Royal Global University, India

Wen-Jun Li

Wen-Jun Li received his PhD in microbiology from Shenyang Institute of Applied Ecology, Chinese Academy of Sciences. He is currently working as Distinguished Professor in School of Life Sciences, Sun Yat-Sen University, Guangzhou, China. His research mainly focuses on microbial diversity under those unusual environments, by using culture-dependent and culture-independent methods, as well as mechanisms of extremophilic microbes to adapt those unusual environments. He was awarded the WFCC (The World Federation for Culture Collections) Skerman award for microbial taxonomy in 2007, and other six provincial and ministry level awards for his outstanding research contributions on the field of microbial systematics and microbial ecology. He has successfully trained more than 150 graduate students and postdoc level students in the field of microbial taxonomy and microbial ecology at home and abroad countries.

Affiliations and expertise

School of Life Sciences, Sun Yat-Sen University, Guangzhou, China

Life Sciences

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Computational Genomics and Structural Bioinformatics in Microbial Science

Microbial Genomics Volume 2

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Javid Ahmad Parray

Niraj Singh

Wen-Jun Li

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