1Preface
524.1.6 Procedure
2Chapter 1. Introduction To Bioinformatics
534.1.7 Alignment
31.1 What is bioinformatics?
544.2 Phylogenetic Tree Construction Methods and Programs
41.2 History
554.2.1 Distance-Based Methods
51.3 Sequences
564.2.2 Character-Based Methods
61.4 Objectives of bioinformatics
574.2.3 Phylogenetic Programs
71.5 Applications
584.3 Exercises
81.6 Exercises
59Chapter 5. Structural Bioinformatics
9Chapter 2. Sequence Alignment
605.1 Basics of Protein Structure
102.1 Aligning sequences pairwise
615.1.1 Amino Acids
112.1.1 Evolutionary Basis
625.1.2 Peptide Formation
122.1.2 Methods
635.1.3 Dihedral Angles
132.1.3 Alignment Algorithms
645.1.4 Hierarchy
142.1.4 Scoring Matrices
655.1.5 Secondary Structures
152.1.5 Statistical Significance of Sequence Alignment
665.1.6 Tertiary Structures
162.2 Searching Similarity in Databases
675.1.7 Determination of Protein Three-Dimensional Structure
172.2.1 Unique Requirements for Database Searching
685.2 Classification, Visualisation and Comparison of Protein structures
182.2.2 Heuristic Database Searching
695.2.1 Protein Structural Visualisation
192.2.3 Basic Local Alignment Search Tool (BLAST)
705.2.2 Protein Structure Comparison
202.2.4 FASTA
715.2.3 Protein Structure Classification
212.2.5 Database Searching with the Smith-Waterman Method
725.3 Predicting secondary protein structures
222.3 Multiple Sequence Alignment
735.3.1 Secondary Structure Prediction for Globular Proteins
232.3.1 Scoring Function
745.3.2 Prediction with Neural Networks
242.3.2 Exhaustive Algorithms
755.3.3 Coiled-Coil Prediction
252.3.3 Heuristic Algorithms
765.4 Predicting Tertiary Structures
262.3.4 Practical Issues
775.4.1 Methods
272.4 Protein Motifs and Domain Prediction
785.4.2 Homology Modeling
282.4.1 Identification of Motifs and Domains in Multiple Sequence Alignment
795.5 Predicting RNA Structure
292.4.2 Motif and Domain Databases using Regular Expressions
805.5.1 Introduction
302.4.3 Motif and Domain Databases using Statistical Models
815.5.2 Types of RNA structures
312.4.4 Protein Family Databases
825.5.3 RNA Secondary Structure Prediction Methods
322.4.6 Sequence Logos
835.6 Exercises
332.5 Exercises
84Chapter 6. Proteomics and Genomics
34Chapter 3. Gene and Promoter Prediction
856.1 Comparing, Assembling and Mapping genomes
353.1 Predicting Genes
866.1.1 Genome Mapping
363.1.1 Categories of Gene Prediction Programs
876.1.2 Genome Sequencing
373.1.2 Gene Prediction in Prokaryotes
886.1.3 Genome Sequence Assembly
383.1.3 Gene Prediction in Eukaryotes
896.1.4 Genome Annotation
393.1.4 Gene Prediction Program
906.1.5 Comparative Genomics
403.2 Predicting Promoter and Regulatory Elements
916.2 Functional Genomics
413.2.1 Promoter and Regulatory Elements in Prokaryotes
926.3 Sequence-Based Approaches
423.2.2 Promoter and Regulatory Elements in Eukaryotes
936.3.1 Expressed Sequence Tags
433.2.3 Prediction Algorithms
946.3.2 Microarray-Based Approaches
443.3 Exercises
956.4 Proteomics
45Chapter 4. Molecular Phylogenetics
966.4.1 The technology of Protein Expression Analysis
464.1 Basics of Phylogenetics
976.4.2 Posttranslational Modifications
474.1.1 Molecular Evolution and Molecular Phylogenetics
986.4.3 Protein-Protein Interactions
484.1.2 Terminology
996.5 Exercises
494.1.3 Gene Phylogeny versus Species Phylogeny
100Appendix
504.1.4 Forms of Tree Representation
101Glossary
514.1.5 Why Finding a True Tree is Difficult?
102Index
