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1.Fundamentals of Genes and Genomes2

1.1 Biological Macromolecules， Genomics， and Bioinformatics2

1.2 DNA as the Universal Genetic Material2

1.3 DNA Double Helix2

1.4 Conformations of DNA5

1.5 Typical Eukaryotic Gene Structure5

1.6 Mutations in the DNA Sequence12

1.7 Some Features of RNA12

1.8 Coding Versus Noncoding RNA14

1.9 Protein Structure and Function15

1.10 Genome Structure and Organization18

References25

2.Fundamentals of Molecular Evolution27

2.1 Bioinformatics， Molecular Evolution， and Phylogenetics27

2.2 Biological Evolution and Basic Premises of Darwinism28

2.3 Molecular Basis of Heritable Genetic Variations—The Raw Materials for Evolution30

2.4 Factors that Affect Gene Frequency in a Population41

2.5 The Neutral Theory of Evolution47

2.6 Molecular Clock Hypothesis in Molecular Evolution49

2.7 Molecular Phylogenetics49

References52

3.Genomic Technologies55

3.1 Advances in Genomics55

3.2 From Sanger Sequencing to Pyrosequencing55

3.3 Pyrosequencing， Mutation Detection，and SNP Genotyping56

3.4 Next-Generation Sequencing Platforms57

3.5 Next-Next-Generation Sequencing Technology61

3.6 High-Density Oligonucleotide-Probe-Based Array to Investigate Genome Expression62

3.7 Genome-Wide Mutagenesis， Genome Editing，and Interference of Genome Expression64

3.8 Special Topic： Optical Mapping of DNA67

References72

4.The Beginning of Bioinformatics73

4.1 Margaret Dayhoff， Richard Eck， Robert Ledley， and the Beginning of Bioinfomatics73

4.2 Definition of Bioinformatics74

4.3 Bioinformatics Versus Computational Biology74

4.4 Goals of Bioinformatic Analysis75

4.5 Bioinformatics Technical Toolbox75

References76

5.Data， Databases， Data Format，Database Search， Data Retrieval Systems，and Genome Browsers78

5.1 Genomic Data78

5.2 Sequence Data Formats78

5.3 Conversion of Sequence Formats Using Readseq79

5.4 Primary Sequence Databases—GenBank， EMBL-Bank，and DDBJ79

5.5 Secondary Databases97

5.6 Some Examples of Publicly Available Secondary and Specialized Databases98

5.7 Data Retrieval101

5.8 An Example of Retrieval of mRNA/Gene Information103

5.9 Data Visualization in Genome Browsers117

5.10 Using Map Viewer to Search the Genome127

5.11 A Note on the State of the Sequence-Assembly Data in Different Databases130

References131

6.Sequence Alignment and Similarity Searching in Genomic Databases： BLAST and FASTA133

6.1 Evolutionary Basis of Sequence Alignment133

6.2 Three Terms-Sequence Identity， Sequence Similarity，and Sequence Homology—And their Proper Usage134

6.3 Sequence Identity and Sequence Similarity135

6.4 Global Versus Local Alignment135

6.5 Pairwise and Multiple Alignment139

6.6 Alignment Algorithms， Gaps， and Gap Penalties140

6.7 Scoring Matrix， Alignment Score， and Statistical Significance of Sequence Alignment144

6.8 Database Searching with the Heuristic Versions of the Smith-Waterman Algorithm—BLAST and FASTA149

6.9 Sequence Comparison， Synteny， and Molecular Evolution155

References155

7.Additional Bioinformatic Analyses Involving Nucleic-Acid Sequences157

7.1 Genome Sequencing157

7.2 Sequence Assembly159

7.3 Genome Annotation160

7.4 Prediction of Promoters， Transcription-Factor-Binding Sites，Translation Initiation Sites， and the ORF167

7.5 Restriction-Site Mapping of the Input Sequence169

7.6 RNA Secondary-Structure Prediction169

7.7 Microarray Analysis173

7.8 Detection of Sequence Polymorphism and the SNP Database176

References181

8.Additional Bioinformatic Analyses Involving Protein Sequences183

8.1 Protein Structure183

8.2 Peptide Bond， Peptide Plane， Bond Rotation， Dihedral Angles， and Ramachandran Plot185

8.3 Prediction of Physicochemical Properties of a Protein186

8.4 Prediction of Protease Digestibility186

8.5 Hydrophobicity， Hydrophilicity， and Antigenicity Prediction， and the Hydropathy Plot186

8.6 Prediction of Post-Translational Modification and Sorting189

8.7 Secondary-Structure Prediction190

8.8 Prediction of Domains and Motifs193

8.9 Viewing the 3D Structure of Proteins （and Other Biological Macromolecules）197

8.10 Allergenic Protein Databases and Protein-Allergenicity Prediction198

8.11 Intrinsically Disordered Protein Analysis203

References206

9.Phylogenetic Analysis209

9.1 Phylogenetics and the Widespread Use of the Phylogenetic Tree209

9.2 Phylogenetic Trees210

9.3 Phylogenetic Analysis Tools211

9.4 Principles of Phylogenetic-Tree Construction211

9.5 Monophyly， Polyphyly， and Paraphyly217

9.6 Species Trees Versus Gene Trees217

References218

Index219