“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. Major topics includes: Photonic DNA computing, knotted proteins problems, mining protein structures, extracting protein-protein interaction from textual data, improving protein-protein interaction in mirrortree method, protein surface modeling and applications, protein electrostatics in hydrogen bond networks, protein side chain packing problem and medical diagnosis in histopathology.