Bioinformatics and RNA

A Practice-Based Approach

Mamta Mittal, Shailendra Singh, Dolly Sharma

• Publisher: CRC Press
• Year: 2021
• Print ISBN:
  9780367619091
• eBook ISBN:
  9781000428384
• Topic: Biological Sciences
• Subtopic: Biology
• Index: Biological Sciences

This book offers a unique balance between a basic introductory knowledge of bioinformatics and a detailed study of algorithmic techniques. Bioinformatics and RNA: A Practice-Based Approach is a complete guide on the fundamental concepts, applications, algorithms, protocols, new trends, challenges, and research results in the area of bioinformatics and RNA.

The book offers a broad introduction to the explosively growing new discipline of bioinformatics. It covers theoretical topics along with computational algorithms. It explores RNA bioinformatics, which contribute to therapeutics and drug discovery. Implementation of algorithms in a DotNet Framework with code and complete insight on the state-of-the-art and recent advancements are presented in detail. The book targets both novice readers as well as practitioners in the field.

FEATURES

• Offers a broad introduction to the explosively growing new discipline of bioinformatics
• Covers theoretical topics and computational algorithms
• Explores RNA bioinformatics to unleash the potential from therapeutics to drug discovery
• Discusses implementation of algorithms in DotNet Frameworks with code
• Presents insights into the state of the art and recent advancements in bioinformatics

The book is useful to undergraduate students with engineering, science, mathematics, or biology backgrounds. Researchers will be equally interested.

1 Introduction to Bioinformatics

1 Introduction to Bioinformatics

The term bioinformatics is a combination of “bio” + “informatics”. Here “Bio” stands for biology and “Informatics” related to information technology. Bioinformatics means informatics techniques are applied to biological problems for finding solutions. The term bioinformatics was coined in 1970 by a Dutch Article. Various researchers have defined bioinformatics as

. . . the study of how information is represented and anlyzed in biological systems, information derived at molecular level [1].

Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale [2].

Bioinformatics has also been stated as a marriage between computer science and molecular biology. Bioinformatics is an inter-disciplinary area of research that integrates biology with information technology, mathematics, statistics, physics and chemistry, as shown in Figure 1.1.

Figure 1.1 Bioinformatics: An Inter-disciplinary Area

Today is the era of big data. A large number of bioinformatics projects subsist today to handle bioinformatics’ big data. The first project of bioinformatics was the Human Genome Project in 1990. The goal of this project was sequencing and annotation of the human genome. Another project, the Celera Genome Project, started in 1998. This project worked on the yeast genome. With the successful completion of these projects, several other projects were initiated; precisely, in 2001, the HapMap Project began.

For carrying out such projects, the need to create, store and communicate huge databases arose. Moreover, biological data was needed in computer-readable form. Consequently, databases like GenBank [3], Ensembl [4], PubMed, M5NR [5], SWISS-PROT [6], OMIM [7], PDB [8], KEGG [9], etc. were coined. Today, large numbers of projects exist for bioinformatics because of the increasing number of researchers in the field of bioinformatics, the explosion of biological data and the increase in the number of funding agencies for projects. There are a number of ongoing projects in various bioinformatics areas like sequence analysis, genomics, structural bioinformatics and computational evolutionary biology. These areas have been illustrated in Figure 1.2.

Figure 1.2 Bioinformatics Areas

1.1 Importance of Bioinformatics

Bioinformatics is everywhere, from disease detection to disease prevention and curation, from the study of microorganisms to the study of all life on earth and from sequence alignment to gene expression.

Following are the important areas and applications of bioinformatics:

• Early detection of diseases
• Diagnose and curation of diseases through RNA interference therapeutics
• Discover uncovered facts of living system
• Tools for handling large-scale biological data
• Study of phlogeny of all life on earth
• Prediction of structure of molecules
• Sequence alignment
• Analyzing the function and structure of genomes
• Hybridization of crops
• Expression, interaction and production of proteins
• DNA sequencing for medicine and forensics
• Different aspects of biotechnology including pharmaceutical and microbiological industries
• Control over diseases through under-expression and over-expression of genes
• Study susceptibility of a person to various diseases through preventive medicine
• Study response of human body of an individual through pharma-co-genomics
• Isolation of genes that enable survival of microorganisms

1.2 DNA, RNA and Protein Sequences

The house of bioinformatics is based on foundation of DNA, RNA and protein. These three are the building blocks of life.

Organisms have cells that communicate and interact to form tissues, organs and organisms. Cells are made of membranes, proteins, carbohydrates, vitamins and nucleic acids. Bunches of cells form tissue. Lots of tissues form an organ and organs make a whole organism.

Assembly of cell parts requires additional information that is contained in deoxyribonucleic acid (DNA). After assembly, the complete functionality of the body is taken care of by proteins. DNA is converted to proteins with RNA (ribonucleic acid) as an intermediate.

1.2.1 DNA

DNA is present inside the nucleus of cell. It is the cookbook for manufacturing proteins. It carries all the genetic information of a cell. Features of DNA are as follows:

• It is a nucleic acid that encodes information necessary to build a cell.
• It contains hereditary information that may be passed from one generation to another. For example, the colour of allele of the child’s eye is the same as that of the mother’s eye.
• It stores and maintains cellular information and passes it from generation to generation.
• It is a cookbook for synthesis of proteins.
• DNA is a stable molecule.
• A single copy of DNA exists per cell.
• DNA replicates itself every time the cell is divided.
• DNA structure
  • DNA is a double helix structure, as shown in Figure 1.3.
  • It contains four bases, namely A for adenine; G for guanine; C for cytosine; and T for thymine.

Figure 1.3 (a) DNA Structure; (b) RNA Structure

1.2.2 RNA

DNA is con...

Table of contents

• Cover
• Half Title
• Series Page
• Title Page
• Copyright Page
• Contents
• Preface
• Authors
• Chapter 1 Introduction to Bioinformatics
• Chapter 2 Computational Biology
• Chapter 3 Phylogenetics
• Chapter 4 RNA
• Chapter 5 Pseudoknot
• Chapter 6 Pseudoknot Prediction Techniques
• Chapter 7 Pseudoknot Grammar
• Chapter 8 New Areas of Bioinformatics
• Glossary
• References
• Index