Bioinformatics and RNA: A Practice-Based Approach

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