A Textbook of Bioinformatics

The following sections are included:

• Dedication
• Contents
• Preface
• Acknowledgments

This section is written as a prelude consisting of a pair of chapters with an objective of learning the fundamental aspects of bioinformatics; hence, relevant introductory notions are narrated and supplemented with underlying concepts, explanatory details, and necessary elaborations. Further, the synergism of interdisciplinary subjects — namely biosciences, informatics, statistics, mathematics, biochemistry, biophysics, technology, engineering, and computer science — forms the focused deliberations outlined in the following two chapters.

Chapter 1: Introduction

Chapter 2: Information Theoretics: A Review

Outlined as the constituent theme of this chapter is a primer on biological science and heuristics of informatic concepts extended to narrate the basics of microbiology that frames the notions of bioinformatics.

Deliberated in this chapter are concepts of entropy vis-à-vis their relation to information-theoretic considerations. Hence, identified are their bioinformatic significance relevant to molecular, cellular, and/or at whole-life systems. Appropriate metrics and measures of information-theory (in Shannon sense) are defined thereof and explained in the contexts of bioinformatics.

Framing informatic details of analytical and computational methods as warranted in bioinformatic studies refer to a synergistic interplay of information-theory, biological concepts, computer science, and medical/health studies. In essence, it is an art of applying information-processing techniques to comprehend the buried knowledge across diverse sets and distinct strata of biosystems. Hence, this section is designed to present (through a pair of chapters), the fundamentals of biomolecular informatics enclaving analytical and computational perspectives extended to biomolecular pairwise/multiple-sequences and next-generation sequencing.

Chapter 3: Biomolecular Informatics

Chapter 4: Pairwise and Multiple Biosequence Analyses and Next-Generation Sequencing

As described in earlier chapters, bioinformatics refers to the pedagogy evolved to analyze and ascertain informatic details in biological sciences. Such details commence at the morsels of genes residing within biomolecular cells and stretch through the entire complexity of whole-life systems. Correspondingly, the gene-related composition of residues in a biosequence represents a statistical structure that poses informative (negentropy) as well as non-informative (posentropy) details. Elucidating such informatic details in biomolecular sequences forms the essential theme of this chapter.

This chapter deals with heuristics of biomolecular sequences extended to address the following bioinformatic tasks: (i) developing dynamic-programming for meaningful alignment of pairwise and multiple biosequences; (ii) prescribing thematic schemes on scoring the integrity of alignments performed; and, (iii) investigating the details of biomolecular sequence via high-throughput sequencing (HTS) schemes (also known as next-generation sequencing, or NGS).

A primary topic of interest in deliberating the notions of bioinformatics refers to understanding the associated resources comprised of databases, information networks, and computational tools. The global set of databases are improvised to store and disseminate the exhaustive bioinformatic data generated and disseminating associated details via modern information networking enable global sharing of such data as needed, in the contexts of bioinformatic studies, and computational tools are prescribed toward thereof to analyze the data and related data mining efforts…

This chapter is devoted to identify and describe various resources, associated information networks, and computational tools adopted in bioinformatics.

Beyond the shores of omic perspectives lies in the horizon of bioinformatics, the so-called translational research informatics (TRI). It forms a unique subdomain of efforts dedicated to address transformational aspects of basic biosciences versus practical considerations usable in macroscopic landscape of biomedical, clinical, and public health sciences. Relevantly transforming the facts of basic sciences into details of health-related studies leads farther into conceivable heuristics of translational and clinical bioinformatics.

In the realm of bioinformatics, two other vital topics of interest that are covered in this section: (1) cytogenetic informatics, a branch of bioinformatics pertinent to entropy perspectives of genetic biology in ascertaining informatic aspects of structures and functions of a biological cell. Furthermore, such organelle level informatic studies include chromosomal synteny details of a cellular complex and (2) viral informatics on ascertaining exclusive omic details framed by viral species, and the associated bioinformatics implies thematic efforts on multiple sequences, for example, of a viral serovar that yield results on identifying the associated motifs useful in rational vaccine designs. Hence, the landscape of this section thus includes the following two chapters:

Chapter 7: Bioinformatics of Cellular Complex and Chromosomal Synteny

Chapter 8: Bioinformatics of Viral Omics

Part I of this chapter describes paradigms of cytogenetic bioinformatics. Relevant entropy details of chromosomal informatics sparsely seen in peer writings, as well as new avenues of bioinformatics at organelle level of the cellular complex.

Addressed in Part II of this chapter are cytogenetic details adopted to ascertain synteny details (appropriately defined via entropic- or information-theoretic metrics) depicting the negentropy features of blocks that represent contiguous genes located within the same chromosome.

Thematic details concerning bioinformatic aspects of viral omics form the scope of this chapter. Analyses based on entropy, energetic, and Fourier spectral domain approaches are indicated thereof to ascertain unique structural features in viral biosequences, and the use of associated motif details gathered on a set of query sequences pertinent to a virus and its serovars is described vis-à-vis rational vaccine design considerations.

Commensurate with classical and modern views on evolution theory pertinent to the origin and diversity of species, details on phylogenetic concepts are presented in this section in the context of bioinformatics. The two chapters presented thereof are:

Chapter 9: Evolution-Theoretics and Phylogeny: An Overview

Chapter 10: Bioinformatic Aspects of Phylogeny

Evolutionary history of organisms concerning the origin and diversity of living systems viewed in the perspectives of morphological, paleontological, and biogeographical phylogeny is the pedagogy outlined in this chapter.

In terms of classical and modern views on evolution theory, phylogenetic concepts and related analyses are described; hence, the heuristics of (re)constructing phylogenetic trees are detailed across the hierarchical span of … gene-to-species.

The following sections are included:

• Bibliography
• Index