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In this broad-based introduction Jonathan Pevsner presents the background theory to bioinformatics. Each chapter includes a problem set, pitfalls, boxes explaining key techniques and mathematics/statistics principles, summary, recommended reading, and a list of freely available software.
List 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.
Summary
The bestselling introduction to bioinformatics and genomics now in its third edition Widely received in its previous editions, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline.
