“Sequence and Genome Analysis II: 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: detecting and associating protein structural motifs to functions, algorithm for identifying structural motifs, Watson-Crick finite automata, annotating and displaying protein sequence logos, extracting and visualizing anatomic structures from volumetric medical images, outlining computational strategies in developing structurally and functionally optimized models, hydrophobicity, surface-based DNA computing, protein secondary structure prediction and DNA detection.