Bioinformatics and Functional Genomics

Part I Analyzing DNA, RNA, and Protein Sequences

1 Introduction 3

2 Access to Sequence Data and Related Information 19

3 Pairwise Sequence Alignment 69

4 Basic Local Alignment Search Tool (BLAST) 121

5 Advanced Database Searching 167

6 Multiple Sequence Alignment 205

7 Molecular Phylogeny and Evolution 245

Part II Genomewide Analysis of DNA, RNA, and Protein

8 DNA: The Eukaryotic Chromosome 307

9 Analysis of Next-Generation Sequence Data 377

10 Bioinformatic Approaches to Ribonucleic Acid (RNA) 433

11 Gene Expression: Microarray and RNA-seq Data Analysis 479

12 Protein Analysis and Proteomics 539

13 Protein Structure 589

14 Functional Genomics 635

Part III Genome Analysis

15 Genomes Across the Tree of Life 699

16 Completed Genomes: Viruses 755

17 Completed Genomes: Bacteria and Archaea 797

18 Eukaryotic Genomes: Fungi 847

19 Eukaryotic Genomes: From Parasites to Primates 887

20 Human Genome 957

21 Human Disease 1011

Glossary 1075

Self-Test Quiz: Solutions 1103

Author Index 1105

Subject Index 1109

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• DNA e Genoma

Bioinformatics; Genomics; Functional genomics; Proteomics; Next-generation sequencing; BLAST; Sequence analysis; Evolution; Phylogeny; Human disease