Table of Contents

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

About the Author

Jonathan Pevsner, PhD, is a Professor in the Department of Neurology at Kennedy Krieger Institute, an internationally recognized institution dedicated to improving the lives of children with neurodevelopmental disorders. He holds a primary faculty appointment as Professor in the Department of Psychiatry and Behavioral Sciences (Johns Hopkins University School of Medicine). He holds joint or secondary appointments in the Department of Neuroscience, the Institute of Genetic Medicine, and the Division of Health Sciences Informatics (Johns Hopkins School of Medicine), and the Department of Molecular Microbiology and Immunology (Johns Hopkins Bloomberg School of Public Health). He has taught bioinformatics courses since 2000 at the Johns Hopkins School of Medicine, and was awarded Teacher of the Year honors by the Graduate Student Association in both 2001 and 2006, the Professors' Award for Excellence in Teaching awarded by the medical faculty (2003), Teacher of the Year (Advanced Academic Programs, 2009), and Teaching Excellence Award in the Johns Hopkins Bloomberg School of Public Health (2011). In 2013 his lab used whole genome sequencing and reported a mutation that causes a rare disease, Sturge-Weber syndrome, as well as a commonly occurring port-wine stain birthmark.