Sequence and Genome Analysis: Methods and Applications provides a comprehensive review and discussion on the key problems in computational biology. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. This book is organized as follows: Chapter 1 discusses Photonic DNA computing, which denotes the nano-scale information technology employing photonics and DNA. Because the activity of a living body is regulated by a variety of bio-molecules such as DNAs, RNAs, and proteins, developing techniques to analyze the bio-molecules efficiently or to control them in flexible ways is a crucial research theme in life science. Photonic DNA computing is therefore resulted. Chapter 2 to Chapter 11 discusses issues related to protein science, which is one of the most popular areas in biochemical and biomedical. The following topics will be addressed: knotted proteins problems (Chapter 2), searching, mining and comparing protein structures (Chapter 3, Chapter 4 and Chapter 5), mining protein-RNA interaction (Chapter 6), extracting protein-protein interaction from textual data (Chapter 7), improving protein-protein in-teraction in mirrortree method (Chapter 8), protein surface modeling and applications (Chapter 9), protein electrostatics in hydrogen bond networks (Chapter 10), and protein side chain packing prob-lem (Chapter 11). Chapter 13 and Chapter 14 discuss "P systems" which is a branch of molecular computing that appears in 2000. These two chapters address important issues such as the theory be-hind P Systems, its implementation detail and its relationship with cell signaling networks. The rest of the book presents some interesting and emerging topics in sequence and genome analysis, which in-cludes discussing medical diagnosis in histopathology (Chapter 15 and 16), evaluating high resolution scanners for imaging of microarray (Chapter 17), reviewing techniques for image processing in biomedical and related areas (Chapter 18 and 19). This book is suitable for advanced undergraduate students and postgraduate students. It takes a practical approach rather than a conceptual approach. It offers a truly reader-friendly way to get to the subject related to sequence and genome analysis, making it the ideal resources for any student who is new to this subject and providing a definitive guide to anyone in this vibrant and evolving discipline.