eChapters

The large volume, type and nature of animal breeding data and the complex nature of analytical requirement warrants additional tools for handling, storage, retrieval and solving complex equations. Accuracy, speed, computational requirement, applicability, etc., has resulted in the development of numerous software exclusive for animal breeding data analysis. The database management system is already explained in the chapter on ‘Nature of animal breeding data and database management’. This chapter gives a note on the commonly used animal breeding software.

Abstract

Bioinformatics is an important interdisciplinary field that brings together several areas of science, including molecular biology, biostatistics, and computer science (vis-a-vis information technology). With the rapid increase in the sequencing of DNA/RNA/protein molecules, as well as the growing understanding of the interconnections between different areas of biological science, the importance of bioinformatics is only increasing. This chapter seems to provide a thorough introduction to the definition, concept, and importance of bioinformatics. It also appears to highlight the relevance and potential scope of the subject for students interested in pursuing a career in the field. As bioinformatics continues to evolve and expand, it is likely to become an increasingly important area of research and development in the life sciences.

Abstract

This chapter provides a brief overview of the key milestones in the development of bioinformatics that would help to understand the historical context and evolution of a subject. As an interdisciplinary field, bioinformatics has grown gradually from molecular biology, with the development of various algorithms, databases, and other important tools that have helped to advance computational biology. Some important events in the history of bioinformatics might include the development of the first algorithms for sequence alignment and comparison, the creation of early databases such as GenBank and Swiss- Prot, and the development of software tools for molecular modeling and drug design. Other key milestones might include the sequencing of the first genomes, the development of high-throughput sequencing technologies, and the emergence of new areas of research such as systems biology and synthetic biology. By understanding the historical context of bioinformatics, students and researchers can gain a deeper appreciation for the current state of the field and the ongoing efforts to advance our understanding of the molecular mechanisms that underlie life.

Abstract

The knowledge of programming language(s) is necessary to solve biocomputational problems and also understand the data pattern. Computer programming is used to develop software to extract information from data which is very crucial while practicing bioinformatics. Programming language is a man-made, computer-understandable, artificial language, that is designed to instruct a machine, particularly a computer to get the desired output. This chapter briefly narrates the concept of algorithms, programming languages, and the historical perspective of the same.

Abstract

Biological databases that are composed of a large collection of digital nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer, which is made available to the research community worldwide using web servers. The vast amount of information generated in molecular biology is analyzed, curated, tabulated, and arranged in databases. There are different types of biological databases, based on their contents. Besides, the database management system, a program to manage the databases, can be of two types: distributed DBMS and relational DBMS. This chapter briefly narrates the importance and purpose of biological databases.

Abstract

Sequence alignment is the positioning of DNA, RNA, or protein sequences with each other to identify the regions of identity, which may be the result of functional, structural, or evolutionary relationships between the sequences. Therefore, sequence alignment is the process of aligning two sequences to achieve the maximum levels of identity and conservation. This chapter deals with the basic concept of sequence alignment and the tools associated with multiple sequence alignment. Further, it describes various matrices used in sequence alignment.

Abstract

Molecular phylogeny is an important method for understanding the evolutionary relationships between different organisms. Molecular phylogeny is based on the idea that organisms that share a more recent common ancestor will have more similarities in their DNA or protein sequences. The chapter seems to cover the basic concepts and terminology used in molecular phylogeny, including the difference between rooted and unrooted trees, as well as various methods used for constructing phylogenetic trees. Further, chapter also covers some common tools and software used for analyzing molecular data and constructing phylogenetic trees. Overall, this chapter provides a useful introduction to molecular phylogeny and the methods used for understanding the evolutionary relationships between different organisms. Understanding these concepts is important for many areas of biological research, including evolutionary biology, ecology, and biotechnology.

Abstract

PCR primer design is a crucial skill for molecular biologists, as it enables the study of gene expression, gene amplification, and molecular markers. Primer3 is an online tool widely used for designing optimal PCR primers, which are pairs of short oligonucleotides that initiate DNA synthesis in vitro using a thermocycler. This tool uses a range of parameters to generate high- quality primers, including target sequence length, melting temperature, GC content, specificity, and product size. Understanding and effectively utilizing these parameters is essential for achieving accurate and reliable PCR results. In this chapter, the practical aspect of primer designing using the online tool Primer3 has been discussed. The parameters and the purpose of their usage have been given in a tabulated manner.

Abstract

Real-time PCR, also known as qPCR, is a highly sensitive technique used to determine the real-time amplification of a target DNA sequence. However, the presence of secondary structures or spurious amplicons can distort the results. When using SYBR Green chemistry, the features of qPCR primers differ from those of standard endpoint PCR primers. As a result, designing primers for SYBR Green qPCR requires extra caution and attention. This chapter outlines the essential features and conditions for designing qPCR primers, including primer length, melting temperature, GC content, specificity, and avoiding primer-dimer formation.

Abstract

The Basic Local Alignment Search Tool, or BLAST, is an online tool provided by the National Center for Biotechnology Information (NCBI) that allows users to search for matches between their query sequences and the sequences stored in NCBI databases. BLAST can be used to search for nucleotide sequences against nucleotide sequences, protein sequences against protein sequences, and protein sequences against translated nucleotide sequences in the databases. BLAST is widely used to study sequence similarity, identify target sequences, analyze the functional aspects of molecular sequences, and investigate evolutionary relationships. This chapter details on the BLAST and its applications.

Abstract

FASTA, which stands for “Fast All”, is a sequence alignment tool developed by William R. Pearson and David J. Lipman in 1985. It is commonly used to identify similarities between DNA and protein sequences. FASTA employs a “hashing” strategy to locate matches for short stretches of identical residues with a length of k, referred to as k-tuples or k-tups. This method enables FASTA to quickly search large databases for sequence similarities, making it a popular tool for identifying homologous sequences, predicting gene functions, and analyzing evolutionary relationships. This chapter elaborates some basics of FASTA.

Abstract

Omics arise from ome which means complete or totality. It refers to the collection of technologies used to investigate the roles, relationships, and actions of the various types of molecules that make up an organism’s cells. Omics technologies provide the tools required to investigate differences in DNA, RNA, proteins, and other cellular molecules between species and individuals within a species. These technologies comprise, genomics, transcriptomics, proteomics, metabolomics, ionomics, glycomics, lipomics, cultureomics, pharmacogenomics, metagenomics, foodomics, eigenomics, phenomics, etc. The inclusion of all omics domain is known as multiomics. In this chapter we describe from basic, type structure of omics to all the recent cutting edge technologies in multiomics.

Abstract

Proteins are complex molecules composed of one or more polypeptide chains made up of amino acid residues. These molecules perform a variety of essential functions in living organisms, including DNA replication, molecule transport, catalyzing metabolic processes, and providing structural support to cells. In this chapter, we explore the four levels of protein structure: primary, secondary, tertiary, and quaternary. Primary structure refers to the specific sequence of amino acids in a polypeptide chain, while secondary structure describes the folding of the chain into alpha-helices, beta-sheets, or other patterns. Tertiary structure is the three-dimensional shape of a single polypeptide chain, and quaternary structure refers to the interactions between multiple polypeptide chains to form a larger protein complex. Additionally, this chapter covers various methods used to predict protein structure, including homology modeling, ab initio prediction, and threading algorithms.

Abstract

When only sequence data is available, homology modeling has become a useful tool for predicting protein structure. Protein structure is often more important than sequence data when evaluating protein function. Homology modeling, also known as comparative modeling, is based on the principle that two sequences that exhibit a high degree of identity or similarity will also share similar structures. This chapter explores the steps involved in homology modeling, including template selection, alignment, model building, refinement, and validation. The Ramachandran plot is a valuable tool for assessing the conformation and bond angles in a protein model, and we discuss its significance in the context of homology modeling. Ultimately, homology modeling is an effective method for predicting protein structure and has numerous applications in protein engineering, drug discovery, and other fields.

Abstract

Molecular modeling is a computational technique used to simulate the three-dimensional interactions between atoms and molecules. It allows for the visualization, manipulation, and prediction of molecular structures and chemical reactions. In this chapter, we discuss the different types of molecular models used in computational chemistry, including ball-and-stick models, space-filling models, wireframe models, and ribbon models. Ball- and-stick models depict atoms as spheres and bonds as sticks. Molecular modeling has numerous applications in drug discovery, materials science, and other fields of research, making it a valuable tool for computational chemists and molecular biologists. Here, this chapter focuses on different types of molecular models.

Abstract

Drug design is a complex computational process that involves studying the structural and physicochemical properties of biological moieties in order to identify new chemical or biochemical substances that can be used as drugs with specific pharmacological properties. The drug discovery pipeline is a crucial aspect of drug design that requires a detailed understanding of the various phases involved. In this chapter, we discuss the fundamental principles and phases of drug design. Additionally, we delve into the concept of docking, a critical step in the drug discovery process that involves predicting the orientation and affinity of a ligand binding to a protein target. The use of computational tools and techniques in drug design has revolutionized the field and is essential for the development of safe and effective drugs.

Abstract

Systems biology is an interdisciplinary field that combines computer and mathematical analysis with biological research to understand the complex interactions within biological systems. This chapter explores the history and evolution of systems biology and its significant impact on modern biology. Systems biology uses a holistic approach to analyze biological systems at the molecular, cellular, and organismal levels, providing a better understanding of biological processes and the interactions between genes, proteins, and other molecules. Systems biology has immense potential in improving human health, agriculture, and the environment, and this chapter explores the ongoing efforts to translate systems biology research into practical applications.

Abstract

Synthetic biology is a multidisciplinary field of study that seeks to understand living systems and organisms, and utilizes engineering principles to design and create new biological components, devices, and systems, as well as modify existing natural systems. This chapter provides an introduction to synthetic biology and describes the procedures and methodologies involved in the design and construction of novel biological systems. The applications of synthetic biology are vast and include the development of biosensors, gene circuits, metabolic pathways, and genetically modified organisms for use in a variety of industries, including healthcare, agriculture, energy, and environmental remediation.

Introduction

As per the reports of the United Nations Organization (UNO), the world population is expected to increase to about 9.7 billion by 2050 and to 10.4 billion by the mid-2080s. The increasing population will result in food scarcity and hunger across the world. To meet the demand for food to feed the people and meet the present aim of WHO of “Zero Hunger by 2030”, agriculture and livestock production needs to be increased. However, according to the ICAR Vision 2050 document, growth of the livestock sector is expected to be higher than the agriculture due to different factors like urbanization and changing food habits among the population residing in the urban area, lack of technology among the small and marginal farmers, reducing operational land, water scarcity, reduced irrigation infrastructure, climate change, etc. to name a few. But to achieve food security through the livestock sector, animal health and production of the animals need to be addressed.

The evolution process took millions of years to develop human and animals on the top of the hierarchy. It has moved forward due to ability to survive the various deadly diseases as for the survival of any leaving creature, it have to overcome the threat posed by the pathogens surviving in its environment and most of the time in its close vicinity. These microbes are smarter than us and are the best example of the survival of the fittest. To overcome these, nature has provided defense system to all leaving creatures that neutralize the invasion of pathogens or undesired microbes. The concept is based on the detection of self and nonself molecules.