This second edition incorporates important advancements made in bioinformatics over the last decade. Focusing on practical problem solving, it works through sequence analysis from simple gene family analysis to expression analysis with microarrays and next-gen sequencing. Using a case study approach, the authors present common bioinformatics problems and introduce the biological and computing concepts that correspond to the type of data being analyzed. For readers without a programming background, this pipeline approach provides the skills to customize existing tools, develop custom tools, and create multiple tool pipelines.