Bioinformatics and RNA: A Practice-Based Approach

Description

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. Cover Half Title Series Page Title Page Copyright Page Contents Preface Authors 1. Introduction to Bioinformatics 1 Introduction to Bioinformatics 1.1 Importance of Bioinformatics 1.2 DNA, RNA and Protein Sequences 1.2.1 DNA 1.2.2 RNA 1.2.3 Protein 1.3 Central Dogma of Molecular Biology 1.4 The Folding Problem 1.5 Genomics and Proteomics 1.5.1 Genomics 1.5.2 Proteomics Appendix 2. Computational Biology 2.1 Sequence Alignment 2.2 Global Sequence Alignment 2.3 Local Sequence Alignment 2.4 Multiple Sequence Alignment Appendix Appendix 3. Phylogenetics 3.1 Introduction to Phylogenetics 3.1.1 Rooted Phylogenetic Tree 3.1.2 Unrooted Phylogenetic Tree 3.2 Molecular Phylogenetics 3.3 Phylogenetic Trees and Their Construction 3.4 Distance Matrix Methods of Phylogenetic Tree Construction 3.4.1 Unweighted Pair Group Method with Arithmetic Mean (UPGMA) - Distance Matrix Method 3.4.2 Neighbor Joining Method - Distance Matrix Method 3.5 Maximum Likelihood - Character-Based Method for Phylogenetic Tree Construction Appendix 4. RNA 4.1 Structure of RNA 4.1.1 Primary Structure of RNA 4.1.2 Secondary Structure of RNA 4.1.3 Tertiary Structure of RNA 4.2 Types of RNA 4.3 Functions of RNA Appendix 5. Pseudoknot 5.1 Definition 5.1.1 Pseudoknot vs Knot 5.1.2 Example of Pseudoknot 5.2 Biological Significance of RNA Pseudoknot 5.3 Representations of a Pseudoknot 5.3.1 Planar Graph Representation 5.3.2 Circular Representation 5.3.3 Dot Bracket Representation 5.3.4 Arc Representation 5.4 Types of Pseudoknots 5.4.1 H-Type Pseudoknot 5.4.2 H-H Type Pseudoknot 5.4.3 H-L Type Pseudoknot 5.4.3.1 H-Lout Type Pseudoknot 5.4.3.2 H-Lin Type Pseudoknot 5.4.4 L-L Type Pseudoknot 5.4.5 Kissing Hairpin Pseudoknot or H-H-H Type Pseudoknot 5.4.6 Three-Knot Pseudoknot 5.4.7 Closed Five-Chain Pseudoknot 5.4.8 Multiloop Pseudoknot 5.4.9 I-Type Pseudoknot 5.4.10 B-Type Pseudoknot Appendix 6. Pseudoknot Prediction Techniques 6.1 Dynamic Programming Technique 6.2 Comparative Sequence Analysis Technique 6.3 Heuristics 6.4 Formal Grammar Technique 6.5 Integer Programming Technique 6.6 Inverse Folding Technique Appendix 7. Pseudoknot Grammar 7.1 Chomsky Hierarchy of Grammars 7.2 Context Free Grammar 7.3 Parallel Communicating Grammar System 7.4 Context Sensitive Grammar 7.5 Pair Stochastic Tree Adjoining Grammar 7.5.1 Substitution 7.5.2 Adjunction 7.6 Multiple Context Free Grammar 7.7 Path Controlled Grammar Appendix 8. New Areas of Bioinformatics 8.1 Drug Target Identification 8.1.1 Target Identification and Validation 8.1.2 Tools for Target Identification and Validation 8.1.3 Target Validation 8.2 Nutrigenomics 8.2.1 Prospects and Applications of Nutrigenomics 8.3 Toxicogenomics 8.4 Bioterrorism 8.4.1 Category A Bioterrorism Agents 8.4.2 Category B Bioterrorism Agents 8.4.3 Category C Bioterrorism Agents 8.4.4 Why Are Biological Weapons or Bioterrorism Agents So Disruptive? 8.4.5 Effects of Biological Attack Appendix Glossary Important Databases References Index